Path to genome folder specified as: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ Using 28 threads for the top and bottom strand indexing processes each, so using 56 cores in total Aligner to be used: >> Bowtie 2 << (default) Writing bisulfite genomes out into a single MFA (multi FastA) file Bismark Genome Preparation - Step I: Preparing folders Path to Bowtie 2 specified as: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ Bisulfite Genome Indexer version v0.21.0 (last modified: 05 Feb 2019) Created Bisulfite Genome folder /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/Bisulfite_Genome/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/Bisulfite_Genome/CT_conversion/ Created Bisulfite Genome folder /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/Bisulfite_Genome/GA_conversion/ Step I - Prepare genome folders - completed Bismark Genome Preparation - Step II: Bisulfite converting reference genome conversions performed: chromosome C->T G->A NC_047559.1 9382222 9356903 NC_047560.1 12183654 12142832 NC_047561.1 9804930 9819422 NC_047562.1 8901860 8890294 NC_047563.1 12209736 12210455 NC_047564.1 10106621 10131005 NC_047565.1 10459327 10474759 NC_047566.1 9761392 9752605 NC_047567.1 6158282 6191616 NC_047568.1 9742640 9724961 NW_022994773.1 21511 20126 NW_022994774.1 195590 194986 NW_022994775.1 21324 21644 NW_022994776.1 19704 20645 NW_022994777.1 20272 20300 NW_022994778.1 128652 128780 NW_022994779.1 19052 19257 NW_022994780.1 19081 18923 NW_022994781.1 17801 19436 NW_022994782.1 17726 18151 NW_022994783.1 17361 16723 NW_022994784.1 225324 225209 NW_022994785.1 17353 18746 NW_022994786.1 14895 16469 NW_022994787.1 14063 13537 NW_022994788.1 13983 14139 NW_022994789.1 123127 123059 NW_022994790.1 13283 13218 NW_022994791.1 12859 12356 NW_022994792.1 12844 11989 NW_022994793.1 10845 10930 NW_022994794.1 118415 115663 NW_022994795.1 10255 9932 NW_022994796.1 10557 10830 NW_022994797.1 11429 11718 NW_022994798.1 10541 10215 NW_022994799.1 115963 115522 NW_022994800.1 9356 10036 NW_022994801.1 8595 10857 NW_022994802.1 8516 9127 NW_022994803.1 7885 8086 NW_022994804.1 7235 8280 NW_022994805.1 112073 109452 NW_022994806.1 7105 5343 NW_022994807.1 5249 5307 NW_022994808.1 5483 5188 NW_022994809.1 105468 104905 NW_022994810.1 5374 5322 NW_022994811.1 4714 4457 NW_022994812.1 4157 4322 NW_022994813.1 103226 104013 NW_022994814.1 3559 2973 NW_022994815.1 92968 90425 NW_022994816.1 161753 159790 NW_022994817.1 520 375 NW_022994818.1 213 217 NW_022994819.1 122599 123827 NW_022994820.1 110423 109946 NW_022994821.1 92891 92810 NW_022994822.1 106251 104080 NW_022994823.1 32414 31197 NW_022994824.1 74907 81462 NW_022994825.1 58493 59382 NW_022994826.1 25332 25265 NW_022994827.1 14107 14477 NW_022994828.1 50047 49957 NW_022994829.1 83778 80930 NW_022994830.1 91443 91497 NW_022994831.1 89431 89854 NW_022994832.1 84031 86157 NW_022994833.1 85415 84819 NW_022994834.1 82812 83650 NW_022994835.1 82170 80786 NW_022994836.1 75160 82337 NW_022994837.1 113875 114803 NW_022994838.1 74893 77621 NW_022994839.1 84806 85329 NW_022994840.1 68158 68594 NW_022994841.1 66119 65094 NW_022994842.1 59104 58736 NW_022994843.1 59265 58818 NW_022994844.1 164192 164153 NW_022994845.1 55277 55687 NW_022994846.1 55183 56857 NW_022994847.1 50455 50449 NW_022994848.1 166325 162723 NW_022994849.1 50103 49481 NW_022994850.1 121428 119466 NW_022994851.1 48269 47978 NW_022994852.1 66400 66797 NW_022994853.1 44284 46204 NW_022994854.1 44647 43809 NW_022994855.1 42428 44856 NW_022994856.1 45007 45717 NW_022994857.1 43259 43225 NW_022994858.1 42433 41363 NW_022994859.1 41653 41789 NW_022994860.1 41889 42384 NW_022994861.1 41202 46060 NW_022994862.1 37600 38761 NW_022994863.1 152306 151510 NW_022994864.1 36922 37539 NW_022994865.1 628630 631896 NW_022994866.1 37977 37959 NW_022994867.1 36330 38472 NW_022994868.1 37200 36797 NW_022994869.1 34881 35587 NW_022994870.1 163919 163321 NW_022994871.1 50805 51289 NW_022994872.1 33121 32816 NW_022994873.1 29156 31388 NW_022994874.1 32931 29492 NW_022994875.1 29580 30249 NW_022994876.1 29076 28653 NW_022994877.1 60431 60816 NW_022994878.1 29390 29440 NW_022994879.1 28789 29573 NW_022994880.1 29617 28111 NW_022994881.1 88006 86518 NW_022994882.1 29389 27924 NW_022994883.1 27476 27777 NW_022994884.1 27124 27276 NW_022994885.1 26932 27230 NW_022994886.1 135279 135072 NW_022994887.1 27894 26080 NW_022994888.1 25403 26605 NW_022994889.1 25255 24849 NW_022994890.1 39913 39253 NW_022994891.1 23748 24682 NW_022994892.1 23527 23559 NW_022994893.1 23212 23228 NW_022994894.1 22650 23913 NW_022994895.1 134595 136749 NW_022994896.1 20209 20044 NW_022994897.1 86748 89839 NW_022994898.1 10212 10584 NW_022994899.1 22332 22587 NW_022994900.1 26041 26075 NW_022994901.1 22600 22549 NW_022994902.1 35518 35427 NW_022994903.1 5574 5245 NW_022994904.1 32538 33184 NW_022994905.1 19485 19606 NW_022994906.1 3978 3921 NW_022994907.1 12911 13497 NW_022994908.1 5699 5812 NW_022994909.1 13299 13122 NW_022994910.1 9804 10389 NW_022994911.1 14417 15463 NW_022994912.1 12619 13127 NW_022994913.1 2998 3249 NW_022994914.1 13721 13004 NW_022994915.1 13638 12774 NW_022994916.1 13419 13537 NW_022994917.1 6498 8142 NW_022994918.1 71545 68923 NW_022994919.1 33416 33184 NW_022994920.1 6295 6326 NW_022994921.1 54863 53542 NW_022994922.1 14106 14900 NW_022994923.1 10169 10587 NW_022994924.1 20950 21686 NW_022994925.1 10972 11119 NW_022994926.1 12993 12870 NW_022994927.1 26899 27093 NW_022994928.1 11452 11433 NW_022994929.1 8244 7907 NW_022994930.1 22923 24000 NW_022994931.1 19743 19028 NW_022994932.1 22103 21180 NW_022994933.1 5308 5280 NW_022994934.1 28024 26752 NW_022994935.1 7714 8304 NW_022994936.1 49774 49730 NW_022994937.1 80988 81912 NW_022994938.1 34085 32882 NW_022994939.1 55303 57785 NW_022994940.1 36851 35982 NW_022994941.1 2970 3040 NW_022994942.1 9406 9508 NW_022994943.1 47618 48122 NW_022994944.1 43010 43640 NW_022994945.1 102507 104999 NW_022994946.1 55162 54365 NW_022994947.1 22240 22160 NW_022994948.1 139744 143196 NW_022994949.1 20465 21470 NW_022994950.1 5410 5158 NW_022994951.1 31997 31433 NW_022994952.1 36952 37258 NW_022994953.1 7531 7280 NW_022994954.1 22733 21617 NW_022994955.1 61350 61396 NW_022994956.1 73072 73301 NW_022994957.1 33815 33345 NW_022994958.1 30667 29282 NW_022994959.1 11378 10636 NW_022994960.1 23121 25534 NW_022994961.1 26067 25935 NW_022994962.1 29189 30458 NW_022994963.1 46603 46548 NW_022994964.1 40417 40181 NW_022994965.1 5420 5737 NW_022994966.1 85155 86753 NW_022994967.1 9261 9292 NW_022994968.1 15135 15208 NW_022994969.1 44242 41711 NW_022994970.1 5295 6510 NW_022994971.1 5583 5482 NW_022994972.1 31760 31760 NW_022994973.1 11490 11249 NW_022994974.1 6045 6086 NW_022994975.1 11296 12374 NW_022994976.1 5434 5361 NW_022994977.1 23088 23929 NW_022994978.1 20082 19321 NW_022994979.1 14493 14159 NW_022994980.1 991 990 NW_022994981.1 9439 10011 NW_022994982.1 25401 25160 NW_022994983.1 13077 13584 NW_022994984.1 6790 6945 NW_022994985.1 32188 32087 NW_022994986.1 23620 23615 NW_022994987.1 51080 50970 NW_022994988.1 5667 4812 NW_022994989.1 25362 24749 NW_022994990.1 5304 5323 NW_022994991.1 39608 40282 NW_022994992.1 17349 17149 NW_022994993.1 38892 37129 NW_022994994.1 3933 3849 NW_022994995.1 10661 10621 NW_022994996.1 16298 16635 NW_022994997.1 49917 50581 NW_022994998.1 8724 9563 NC_001276.1 2672 4007 Total number of conversions performed: C->T: 108502499 G->A: 108517078 Step II - Genome bisulfite conversions - completed Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer Please be aware that this process can - depending on genome size - take several hours! Preparing indexing of CT converted genome in /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/Bisulfite_Genome/CT_conversion/ Parent process: Starting to index C->T converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.CT_conversion.fa BS_CT --threads 28 Settings: Output files: "BS_CT.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 112 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.CT_conversion.fa Building a SMALL index Reading reference sizes Preparing indexing of GA converted genome in /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/Bisulfite_Genome/GA_conversion/ Child process: Starting to index G->A converted genome with the following command: /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2-build -f genome_mfa.GA_conversion.fa BS_GA --threads 28 Settings: Output files: "BS_GA.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 112 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome_mfa.GA_conversion.fa Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 bmax according to bmaxDivN setting: 5784692 Using parameters --bmax 4338519 --dcv 1024 Doing ahead-of-time memory usage test Time to join reference sequences: 00:00:03 bmax according to bmaxDivN setting: 5784692 Using parameters --bmax 4338519 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 4338519 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples Passed! Constructing with these parameters: --bmax 4338519 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:05 Allocating rank array Ranking v-sort output V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:05 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Invoking Larsson-Sadakane on ranks time: 00:00:06 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 35, merged 127; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 38, merged 132; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 18, merged 15; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 22, merged 15; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 6; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 11, merged 10; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 3, merged 8; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 3.04172e+06 (target: 4338518) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 213 Getting block 2 of 213 Getting block 3 of 213 Reserving size (4338519) for bucket 1 Getting block 4 of 213 Reserving size (4338519) for bucket 2 Reserving size (4338519) for bucket 3 Getting block 5 of 213 Getting block 6 of 213 Getting block 7 of 213 Getting block 8 of 213 Getting block 9 of 213 Getting block 10 of 213 Getting block 11 of 213 Getting block 12 of 213 Getting block 13 of 213 Getting block 14 of 213 Getting block 15 of 213 Getting block 16 of 213 Getting block 17 of 213 Getting block 18 of 213 Getting block 19 of 213 Getting block 20 of 213 Getting block 21 of 213 Getting block 22 of 213 Calculating Z arrays for bucket 1 Reserving size (4338519) for bucket 4 Getting block 23 of 213 Getting block 24 of 213 Getting block 25 of 213 Getting block 26 of 213 Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 3 Reserving size (4338519) for bucket 5 Reserving size (4338519) for bucket 6 Reserving size (4338519) for bucket 7 Reserving size (4338519) for bucket 8 Reserving size (4338519) for bucket 9 Reserving size (4338519) for bucket 10 Reserving size (4338519) for bucket 11 Reserving size (4338519) for bucket 12 Reserving size (4338519) for bucket 13 Reserving size (4338519) for bucket 14 Reserving size (4338519) for bucket 15 Reserving size (4338519) for bucket 16 Reserving size (4338519) for bucket 17 Reserving size (4338519) for bucket 18 Reserving size (4338519) for bucket 19 Reserving size (4338519) for bucket 20 Reserving size (4338519) for bucket 21 Reserving size (4338519) for bucket 22 Getting block 27 of 213 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 4 Reserving size (4338519) for bucket 23 Reserving size (4338519) for bucket 24 Reserving size (4338519) for bucket 25 Reserving size (4338519) for bucket 26 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 9 Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 22 Reserving size (4338519) for bucket 27 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 8: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 27: Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 2; iterating... Avg bucket size: 3.08517e+06 (target: 4338518) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 210 Reserving size (4338519) for bucket 1 Getting block 2 of 210 Getting block 3 of 210 Getting block 4 of 210 Getting block 5 of 210 Getting block 6 of 210 Getting block 7 of 210 Getting block 8 of 210 Getting block 9 of 210 Getting block 10 of 210 Getting block 11 of 210 Getting block 12 of 210 Getting block 13 of 210 Getting block 14 of 210 Getting block 15 of 210 Calculating Z arrays for bucket 1 Reserving size (4338519) for bucket 2 Getting block 16 of 210 Getting block 17 of 210 Getting block 18 of 210 Getting block 19 of 210 Getting block 20 of 210 Getting block 21 of 210 Getting block 22 of 210 Getting block 23 of 210 Getting block 24 of 210 Getting block 25 of 210 Getting block 26 of 210 Getting block 27 of 210 Reserving size (4338519) for bucket 3 Reserving size (4338519) for bucket 4 Reserving size (4338519) for bucket 5 Reserving size (4338519) for bucket 6 Reserving size (4338519) for bucket 7 Reserving size (4338519) for bucket 8 Reserving size (4338519) for bucket 9 Reserving size (4338519) for bucket 10 Reserving size (4338519) for bucket 11 Reserving size (4338519) for bucket 12 Reserving size (4338519) for bucket 13 Reserving size (4338519) for bucket 14 Reserving size (4338519) for bucket 15 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Reserving size (4338519) for bucket 16 Reserving size (4338519) for bucket 17 Reserving size (4338519) for bucket 18 Reserving size (4338519) for bucket 19 Reserving size (4338519) for bucket 20 Reserving size (4338519) for bucket 21 Reserving size (4338519) for bucket 22 Reserving size (4338519) for bucket 23 Reserving size (4338519) for bucket 24 Reserving size (4338519) for bucket 25 Reserving size (4338519) for bucket 26 Reserving size (4338519) for bucket 27 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 16 Entering block accumulator loop for bucket 2: Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 25: Entering block 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bucket 9: 70% bucket 5: 80% bucket 14: 70% bucket 3: 70% bucket 8: 70% bucket 6: 90% bucket 11: 70% bucket 19: 70% bucket 15: 70% bucket 16: 60% bucket 26: 60% bucket 25: 60% bucket 27: 60% bucket 17: 70% bucket 10: 70% bucket 13: 70% bucket 10: 70% bucket 18: 60% bucket 12: 80% bucket 1: 90% bucket 1: 70% bucket 18: 70% bucket 20: 70% bucket 8: 80% bucket 17: 70% bucket 5: 70% bucket 2: 80% bucket 22: 80% bucket 24: 70% bucket 4: 70% bucket 2: 70% bucket 21: 80% bucket 27: 70% bucket 11: 70% bucket 6: 70% bucket 4: 80% bucket 22: 80% bucket 14: 70% bucket 19: 70% bucket 13: 70% bucket 14: 80% bucket 23: 70% bucket 16: 80% bucket 5: 90% bucket 26: 70% bucket 25: 70% bucket 7: 80% bucket 9: 80% bucket 24: 70% bucket 20: 70% bucket 21: 70% bucket 9: 80% bucket 3: 80% bucket 7: 80% bucket 6: 100% Sorting block of length 1895145 for bucket 6 (Using difference cover) bucket 3: 80% bucket 8: 80% bucket 23: 80% bucket 11: 80% bucket 15: 80% bucket 12: 80% bucket 15: 80% bucket 1: 100% Sorting block of length 3653101 for bucket 1 (Using difference cover) bucket 10: 80% bucket 19: 80% bucket 25: 70% bucket 16: 70% bucket 10: 80% bucket 13: 80% bucket 5: 80% bucket 12: 90% bucket 26: 70% bucket 14: 80% bucket 17: 80% bucket 1: 80% bucket 18: 80% bucket 27: 70% bucket 20: 80% bucket 4: 90% bucket 2: 90% bucket 18: 70% bucket 17: 80% bucket 8: 90% bucket 14: 90% bucket 21: 90% bucket 22: 90% bucket 24: 80% bucket 2: 80% bucket 4: 80% bucket 11: 80% bucket 6: 80% bucket 27: 80% bucket 19: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 2965315 for bucket 5 (Using difference cover) bucket 16: 90% bucket 13: 80% bucket 22: 90% bucket 23: 80% bucket 7: 90% bucket 26: 80% bucket 3: 90% bucket 9: 90% bucket 8: 90% bucket 9: 90% bucket 11: 90% bucket 7: 90% bucket 3: 90% bucket 25: 80% bucket 26: 80% bucket 24: 80% bucket 14: 90% bucket 21: 80% bucket 20: 80% bucket 15: 90% bucket 12: 90% bucket 13: 90% bucket 15: 90% bucket 23: 90% bucket 12: 100% Sorting block of length 645291 for bucket 12 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1895146 for bucket 6 bucket 10: 90% bucket 19: 90% Getting block 28 of 210 Reserving size (4338519) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 10: 90% bucket 25: 80% bucket 4: 100% Sorting block of length 4027962 for bucket 4 (Using difference cover) bucket 2: 100% Sorting block of length 3511993 for bucket 2 (Using difference cover) bucket 16: 80% bucket 1: 90% bucket 18: 90% bucket 17: 90% bucket 20: 90% bucket 17: 90% bucket 14: 100% Sorting block of length 472540 for bucket 14 (Using difference cover) bucket 8: 100% Sorting block of length 3087451 for bucket 8 (Using difference cover) bucket 27: 80% bucket 21: 100% Sorting block of length 1921182 for bucket 21 (Using difference cover) bucket 18: 80% bucket 3: 100% Sorting block of length 4253685 for bucket 3 (Using difference cover) Sorting block time: 00:00:00 Returning block of 645292 for bucket 12 bucket 26: 90% Getting block 29 of 210 Reserving size (4338519) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 22: 100% Sorting block of length 2626537 for bucket 22 (Using difference cover) bucket 24: 90% bucket 2: 90% bucket 4: 90% bucket 19: 90% bucket 6: 90% bucket 16: 100% Sorting block of length 3580530 for bucket 16 (Using difference cover) bucket 11: 90% bucket 5: 100% Sorting block of length 1386998 for bucket 5 (Using difference cover) bucket 27: 90% bucket 26: 90% bucket 7: 100% Sorting block of length 3044589 for bucket 7 (Using difference cover) bucket 9: 100% Sorting block of length 3195499 for bucket 9 (Using difference cover) bucket 13: 100% Sorting block of length 4445333 for bucket 13 (Using difference cover) Sorting block time: 00:00:00 Returning block of 472541 for bucket 14 Getting block 30 of 210 Reserving size (4338519) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: bucket 8: 100% Sorting block of length 2728657 for bucket 8 (Using difference cover) bucket 23: 90% bucket 13: 90% bucket 11: 100% Sorting block of length 3920635 for bucket 11 (Using difference cover) bucket 22: 100% Sorting block of length 3174751 for bucket 22 (Using difference cover) bucket 1: 100% Sorting block of length 3504714 for bucket 1 (Using difference cover) bucket 9: 100% Sorting block of length 1611161 for bucket 9 (Using difference cover) bucket 17: 100% Sorting block of length 2642362 for bucket 17 (Using difference cover) bucket 3: 100% Sorting block of length 1773899 for bucket 3 (Using difference cover) bucket 7: 100% Sorting block of length 1441375 for bucket 7 (Using difference cover) bucket 15: 100% Sorting block of length 2492322 for bucket 15 (Using difference cover) bucket 10: 100% Sorting block of length 3880686 for bucket 10 (Using difference cover) bucket 14: 100% Sorting block of length 3467590 for bucket 14 (Using difference cover) bucket 12: 100% Sorting block of length 2540791 for bucket 12 (Using difference cover) bucket 18: 100% Sorting block of length 3090354 for bucket 18 (Using difference cover) bucket 25: 90% bucket 20: 90% bucket 24: 90% bucket 20: 100% Sorting block of length 3226203 for bucket 20 (Using difference cover) bucket 21: 90% bucket 23: 100% Sorting block of length 2517970 for bucket 23 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3653102 for bucket 1 bucket 15: 100% Sorting block of length 2403490 for bucket 15 (Using difference cover) bucket 24: 100% Sorting block of length 1598264 for bucket 24 (Using difference cover) bucket 19: 100% Sorting block of length 2604957 for bucket 19 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2965316 for bucket 5 bucket 10: 100% Sorting block of length 3508497 for bucket 10 (Using difference cover) Getting block 31 of 210 Reserving size (4338519) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 27: 100% Sorting block of length 2909719 for bucket 27 (Using difference cover) bucket 28: 10% bucket 25: 90% Getting block 32 of 210 Reserving size (4338519) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 19: 100% Sorting block of length 378387 for bucket 19 (Using difference cover) bucket 23: 100% Sorting block of length 4226903 for bucket 23 (Using difference cover) bucket 16: 90% bucket 17: 100% Sorting block of length 1739522 for bucket 17 (Using difference cover) bucket 2: 100% Sorting block of length 4101333 for bucket 2 (Using difference cover) bucket 18: 90% bucket 27: 90% Sorting block time: 00:00:01 Returning block of 1921183 for bucket 21 bucket 29: 10% bucket 6: 100% Sorting block of length 3112309 for bucket 6 (Using difference cover) bucket 26: 100% Sorting block of length 3704931 for bucket 26 (Using difference cover) Getting block 33 of 210 Reserving size (4338519) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: bucket 4: 100% Sorting block of length 4197354 for bucket 4 (Using difference cover) Sorting block time: 00:00:01 Returning block of 378388 for bucket 19 Getting block 28 of 213 Reserving size (4338519) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 11: 100% Sorting block of length 3175952 for bucket 11 (Using difference cover) bucket 25: 100% Sorting block of length 3000408 for bucket 25 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1386999 for bucket 5 bucket 13: 100% Sorting block of length 2293706 for bucket 13 (Using difference cover) Getting block 29 of 213 Reserving size (4338519) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 26: 100% Sorting block of length 2639630 for bucket 26 (Using difference cover) bucket 27: 100% Sorting block of length 3817105 for bucket 27 (Using difference cover) bucket 18: 100% Sorting block of length 4112609 for bucket 18 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1441376 for bucket 7 bucket 30: 10% Sorting block time: 00:00:01 Returning block of 1611162 for bucket 9 bucket 24: 100% Sorting block of length 2135695 for bucket 24 (Using difference cover) Getting block 30 of 213 Reserving size (4338519) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:02 Returning block of 3511994 for bucket 2 Getting block 31 of 213 Reserving size (4338519) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 20: 100% Sorting block of length 4003337 for bucket 20 (Using difference cover) bucket 21: 100% Sorting block of length 2264945 for bucket 21 (Using difference cover) Getting block 34 of 210 Reserving size (4338519) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 31: 10% bucket 25: 100% Sorting block of length 3612335 for bucket 25 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1773900 for bucket 3 Getting block 32 of 213 Reserving size (4338519) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 16: 100% Sorting block of length 2828352 for bucket 16 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2626538 for bucket 22 Sorting block time: 00:00:02 Returning block of 1598265 for bucket 24 Getting block 35 of 210 Reserving size (4338519) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Getting block 36 of 210 Reserving size (4338519) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:02 Returning block of 1739523 for bucket 17 Getting block 33 of 213 Reserving size (4338519) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:02 Returning block of 3090355 for bucket 18 Sorting block time: 00:00:02 Returning block of 3226204 for bucket 20 Getting block 37 of 210 Reserving size (4338519) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:03 Returning block of 4027963 for bucket 4 bucket 28: 20% Sorting block time: 00:00:03 Returning block of 2728658 for bucket 8 bucket 32: 10% Getting block 38 of 210 Reserving size (4338519) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Sorting block time: 00:00:03 Returning block of 3087452 for bucket 8 Sorting block time: 00:00:02 Returning block of 2540792 for bucket 12 bucket 28: 10% Sorting block time: 00:00:03 Returning block of 3044590 for bucket 7 Sorting block time: 00:00:02 Returning block of 2642363 for bucket 17 Getting block 39 of 210 Reserving size (4338519) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 34 of 213 Reserving size (4338519) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Getting block 40 of 210 Reserving size (4338519) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 35 of 213 Reserving size (4338519) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: bucket 33: 10% bucket 29: 20% Sorting block time: 00:00:03 Returning block of 2517971 for bucket 23 Getting block 41 of 210 Reserving size (4338519) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:04 Returning block of 3195500 for bucket 9 Sorting block time: 00:00:02 Returning block of 3112310 for bucket 6 Getting block 42 of 210 Reserving size (4338519) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:03 Returning block of 2403491 for bucket 15 bucket 29: 10% Getting block 36 of 213 Reserving size (4338519) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 43 of 210 Reserving size (4338519) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Sorting block time: 00:00:03 Returning block of 2492323 for bucket 15 Getting block 37 of 213 Reserving size (4338519) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:03 Returning block of 3174752 for bucket 22 Getting block 38 of 213 Reserving size (4338519) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Sorting block time: 00:00:03 Returning block of 3504715 for bucket 1 Sorting block time: 00:00:04 Returning block of 4253686 for bucket 3 bucket 31: 10% Sorting block time: 00:00:04 Returning block of 3580531 for bucket 16 Getting block 44 of 210 Reserving size (4338519) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Getting block 39 of 213 Reserving size (4338519) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Sorting block time: 00:00:03 Returning block of 2604958 for bucket 19 Sorting block time: 00:00:04 Returning block of 4445334 for bucket 13 Sorting block time: 00:00:03 Returning block of 3880687 for bucket 10 Getting block 40 of 213 Reserving size (4338519) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Sorting block time: 00:00:02 Returning block of 3000409 for bucket 25 Getting block 45 of 210 Reserving size (4338519) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 210 Reserving size (4338519) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 47 of 210 Reserving size (4338519) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 30: 20% Getting block 41 of 213 Reserving size (4338519) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Getting block 48 of 210 Reserving size (4338519) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: bucket 30: 10% bucket 32: 10% Getting block 49 of 210 Reserving size (4338519) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Sorting block time: 00:00:03 Returning block of 3467591 for bucket 14 Sorting block time: 00:00:02 Returning block of 2293707 for bucket 13 Getting block 42 of 213 Reserving size (4338519) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Sorting block time: 00:00:02 Returning block of 2135696 for bucket 24 Getting block 43 of 213 Reserving size (4338519) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Sorting block time: 00:00:03 Returning block of 3508498 for bucket 10 Getting block 44 of 213 Reserving size (4338519) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: bucket 31: 20% Sorting block time: 00:00:04 Returning block of 2909720 for bucket 27 Sorting block time: 00:00:04 Returning block of 3920636 for bucket 11 Sorting block time: 00:00:03 Returning block of 2264946 for bucket 21 bucket 36: 10% bucket 33: 10% Getting block 50 of 210 Reserving size (4338519) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 45 of 213 Reserving size (4338519) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Getting block 46 of 213 Reserving size (4338519) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Getting block 51 of 210 Reserving size (4338519) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: Sorting block time: 00:00:03 Returning block of 4197355 for bucket 4 Sorting block time: 00:00:03 Returning block of 2639631 for bucket 26 bucket 34: 10% Sorting block time: 00:00:03 Returning block of 3175953 for bucket 11 Getting block 52 of 210 Reserving size (4338519) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 35: 10% Getting block 47 of 213 Reserving size (4338519) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: Sorting block time: 00:00:04 Returning block of 4101334 for bucket 2 bucket 34: 10% bucket 35: 10% bucket 28: 20% bucket 38: 10% Getting block 48 of 213 Reserving size (4338519) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Sorting block time: 00:00:04 Returning block of 4226904 for bucket 23 bucket 32: 20% Getting block 49 of 213 Reserving size (4338519) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: bucket 29: 20% bucket 36: 10% Sorting block time: 00:00:03 Returning block of 3817106 for bucket 27 Getting block 53 of 210 Reserving size (4338519) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: Sorting block time: 00:00:03 Returning block of 3704932 for bucket 26 bucket 37: 10% bucket 29: 30% bucket 31: 20% Getting block 50 of 213 Reserving size (4338519) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 37: 10% bucket 40: 10% Getting block 51 of 213 Reserving size (4338519) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 33: 20% bucket 39: 10% bucket 28: 30% Sorting block time: 00:00:03 Returning block of 2828353 for bucket 16 bucket 41: 10% bucket 39: 10% bucket 30: 20% Getting block 52 of 213 Reserving size (4338519) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 46: 10% bucket 30: 30% bucket 42: 10% Sorting block time: 00:00:03 Returning block of 3612336 for bucket 25 bucket 42: 10% Sorting block time: 00:00:04 Returning block of 4112610 for bucket 18 bucket 41: 10% bucket 43: 10% bucket 40: 10% bucket 43: 10% bucket 32: 20% bucket 44: 10% bucket 45: 10% Getting block 54 of 210 Reserving size (4338519) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: Getting block 53 of 213 Reserving size (4338519) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 36: 20% bucket 31: 30% bucket 38: 10% bucket 33: 20% bucket 44: 10% Sorting block time: 00:00:04 Returning block of 4003338 for bucket 20 bucket 45: 10% bucket 48: 10% Getting block 54 of 213 Reserving size (4338519) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 49: 10% bucket 35: 20% bucket 28: 30% bucket 47: 10% bucket 50: 10% bucket 46: 10% bucket 34: 20% bucket 47: 10% bucket 29: 30% bucket 38: 20% bucket 32: 30% bucket 49: 10% bucket 34: 20% bucket 31: 30% bucket 48: 10% bucket 36: 20% bucket 35: 20% bucket 50: 10% bucket 53: 10% bucket 40: 20% bucket 41: 20% bucket 51: 10% bucket 51: 10% bucket 37: 20% bucket 39: 20% bucket 37: 20% bucket 30: 30% bucket 29: 40% bucket 46: 20% bucket 28: 40% bucket 28: 40% bucket 42: 20% bucket 53: 10% bucket 33: 30% bucket 52: 10% bucket 52: 10% bucket 39: 20% bucket 43: 20% bucket 33: 30% bucket 44: 20% bucket 44: 20% bucket 45: 20% bucket 48: 20% bucket 45: 20% bucket 49: 20% bucket 42: 20% bucket 30: 40% bucket 35: 30% bucket 29: 40% bucket 38: 30% bucket 32: 30% bucket 32: 40% bucket 54: 10% bucket 34: 30% bucket 36: 30% bucket 31: 40% bucket 47: 20% bucket 43: 20% bucket 31: 40% bucket 36: 30% bucket 40: 30% bucket 50: 20% bucket 54: 10% bucket 41: 30% bucket 41: 20% bucket 34: 30% bucket 39: 30% bucket 37: 30% bucket 51: 20% bucket 38: 20% bucket 47: 20% bucket 30: 40% bucket 35: 30% bucket 46: 20% bucket 53: 20% bucket 40: 20% bucket 28: 50% bucket 46: 30% bucket 50: 20% bucket 29: 50% bucket 49: 30% bucket 49: 20% bucket 42: 30% bucket 43: 30% bucket 44: 30% bucket 48: 20% bucket 33: 40% bucket 34: 40% bucket 44: 30% bucket 48: 30% bucket 45: 30% bucket 51: 20% bucket 53: 20% bucket 37: 30% bucket 52: 20% bucket 35: 40% bucket 28: 50% bucket 29: 50% bucket 32: 50% bucket 38: 40% bucket 31: 50% bucket 45: 30% bucket 30: 50% bucket 39: 30% bucket 54: 20% bucket 43: 30% bucket 36: 40% bucket 36: 40% bucket 47: 30% bucket 42: 30% bucket 40: 40% bucket 32: 40% bucket 50: 30% bucket 39: 40% bucket 41: 40% bucket 30: 50% bucket 51: 30% bucket 37: 40% bucket 28: 60% bucket 33: 40% bucket 35: 40% bucket 53: 30% bucket 54: 20% bucket 46: 40% bucket 31: 50% bucket 52: 20% bucket 43: 40% bucket 49: 40% bucket 42: 40% bucket 34: 40% bucket 33: 50% bucket 47: 30% bucket 34: 50% bucket 44: 40% bucket 48: 40% bucket 44: 40% bucket 45: 40% bucket 49: 30% bucket 35: 50% bucket 50: 30% bucket 52: 30% bucket 29: 60% bucket 29: 60% bucket 32: 60% bucket 31: 60% bucket 38: 50% bucket 46: 30% bucket 40: 30% bucket 36: 50% bucket 39: 40% bucket 47: 40% bucket 41: 30% bucket 54: 30% bucket 40: 50% bucket 28: 60% bucket 36: 50% bucket 48: 30% bucket 50: 40% bucket 39: 50% bucket 30: 60% bucket 41: 50% bucket 37: 50% bucket 32: 50% bucket 43: 40% bucket 51: 40% bucket 38: 30% bucket 28: 70% bucket 30: 60% bucket 42: 40% bucket 51: 30% bucket 45: 40% bucket 53: 30% bucket 37: 40% bucket 53: 40% bucket 43: 50% bucket 46: 50% bucket 35: 50% bucket 33: 60% bucket 49: 50% bucket 42: 50% bucket 34: 60% bucket 44: 50% bucket 48: 50% bucket 35: 60% bucket 45: 50% bucket 54: 30% bucket 29: 70% bucket 31: 70% bucket 52: 40% bucket 33: 50% bucket 31: 60% bucket 32: 70% bucket 44: 50% bucket 38: 60% bucket 36: 60% bucket 49: 40% bucket 34: 50% bucket 47: 50% bucket 40: 60% bucket 54: 40% bucket 39: 60% bucket 50: 50% bucket 29: 70% bucket 30: 70% bucket 37: 60% bucket 39: 50% bucket 50: 40% bucket 47: 40% bucket 41: 60% bucket 28: 80% bucket 36: 60% bucket 52: 30% bucket 51: 50% bucket 48: 40% bucket 40: 40% bucket 30: 70% bucket 43: 60% bucket 53: 50% bucket 46: 40% bucket 28: 70% bucket 46: 60% bucket 34: 70% bucket 33: 70% bucket 49: 60% bucket 42: 60% bucket 44: 60% bucket 35: 70% bucket 48: 60% bucket 41: 40% bucket 45: 60% bucket 45: 50% bucket 29: 80% bucket 31: 80% bucket 42: 50% bucket 51: 40% bucket 32: 80% bucket 52: 50% bucket 31: 70% bucket 38: 70% bucket 35: 60% bucket 43: 50% bucket 36: 70% bucket 32: 60% bucket 44: 60% bucket 40: 70% bucket 47: 60% bucket 53: 40% bucket 38: 40% bucket 54: 40% bucket 39: 70% bucket 30: 80% bucket 50: 60% bucket 54: 50% bucket 37: 70% bucket 34: 60% bucket 28: 90% bucket 37: 50% bucket 41: 70% bucket 29: 80% bucket 39: 60% bucket 43: 70% bucket 51: 60% bucket 33: 60% bucket 53: 60% bucket 34: 80% bucket 33: 80% bucket 30: 80% bucket 46: 70% bucket 44: 70% bucket 35: 80% bucket 49: 70% bucket 42: 70% bucket 48: 70% bucket 28: 80% bucket 29: 90% bucket 31: 90% bucket 45: 70% bucket 36: 70% bucket 32: 90% bucket 40: 50% bucket 47: 50% bucket 38: 80% bucket 35: 70% bucket 49: 50% bucket 46: 50% bucket 51: 50% bucket 52: 60% bucket 36: 80% bucket 43: 60% bucket 40: 80% bucket 48: 50% bucket 42: 60% bucket 47: 70% bucket 44: 70% bucket 39: 80% bucket 30: 90% bucket 45: 60% bucket 50: 50% bucket 50: 70% bucket 37: 80% bucket 28: 100% Sorting block of length 4192811 for bucket 28 (Using difference cover) bucket 54: 60% bucket 43: 80% bucket 52: 40% bucket 41: 80% bucket 34: 90% bucket 51: 70% bucket 32: 70% bucket 37: 60% bucket 33: 90% bucket 39: 70% bucket 29: 90% bucket 54: 50% bucket 53: 70% bucket 46: 80% bucket 44: 80% bucket 38: 50% bucket 35: 90% bucket 42: 80% bucket 30: 90% bucket 31: 80% bucket 49: 80% bucket 29: 100% Sorting block of length 3403331 for bucket 29 (Using difference cover) bucket 48: 80% bucket 31: 100% Sorting block of length 3070194 for bucket 31 (Using difference cover) bucket 53: 50% bucket 41: 50% bucket 34: 70% bucket 45: 80% bucket 28: 90% bucket 33: 70% bucket 32: 100% Sorting block of length 4021310 for bucket 32 (Using difference cover) bucket 35: 80% bucket 38: 90% bucket 36: 90% bucket 52: 70% bucket 40: 90% bucket 39: 90% bucket 30: 100% Sorting block of length 1471295 for bucket 30 (Using difference cover) bucket 47: 80% bucket 51: 60% bucket 44: 80% bucket 36: 80% bucket 37: 90% bucket 50: 80% bucket 46: 60% bucket 47: 60% bucket 42: 70% bucket 43: 90% bucket 40: 60% bucket 45: 70% bucket 43: 70% bucket 54: 70% bucket 41: 90% bucket 34: 100% Sorting block of length 3772822 for bucket 34 (Using difference cover) bucket 33: 100% Sorting block of length 3470008 for bucket 33 (Using difference cover) bucket 53: 80% bucket 51: 80% bucket 35: 100% Sorting block of length 3587971 for bucket 35 (Using difference cover) bucket 44: 90% bucket 46: 90% bucket 37: 70% bucket 42: 90% bucket 48: 90% bucket 49: 90% bucket 50: 60% bucket 39: 80% bucket 32: 80% bucket 49: 60% bucket 29: 100% Sorting block of length 2208003 for bucket 29 (Using difference cover) bucket 45: 90% bucket 30: 100% Sorting block of length 4071346 for bucket 30 (Using difference cover) bucket 48: 60% bucket 54: 60% bucket 38: 100% Sorting block of length 3383924 for bucket 38 (Using difference cover) bucket 36: 100% Sorting block of length 2403800 for bucket 36 (Using difference cover) bucket 28: 100% Sorting block of length 4253235 for bucket 28 (Using difference cover) bucket 34: 80% Sorting block time: 00:00:01 Returning block of 1471296 for bucket 30 bucket 31: 90% Getting block 55 of 213 Reserving size (4338519) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 40: 100% Sorting block of length 3872809 for bucket 40 (Using difference cover) bucket 35: 90% bucket 52: 80% bucket 41: 60% bucket 39: 100% Sorting block of length 955393 for bucket 39 (Using difference cover) bucket 47: 90% bucket 52: 50% bucket 51: 70% bucket 37: 100% Sorting block of length 4317752 for bucket 37 (Using difference cover) bucket 38: 60% bucket 53: 60% bucket 50: 90% bucket 33: 80% bucket 43: 100% Sorting block of length 363653 for bucket 43 (Using difference cover) bucket 44: 90% bucket 36: 90% bucket 41: 100% Sorting block of length 4202132 for bucket 41 (Using difference cover) bucket 54: 80% bucket 53: 90% Sorting block time: 00:00:00 Returning block of 363654 for bucket 43 Getting block 56 of 213 Reserving size (4338519) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Sorting block time: 00:00:03 Returning block of 3070195 for bucket 31 bucket 51: 90% bucket 44: 100% Sorting block of length 2541907 for bucket 44 (Using difference cover) Sorting block time: 00:00:01 Returning block of 955394 for bucket 39 bucket 46: 100% Sorting block of length 3899542 for bucket 46 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4192812 for bucket 28 bucket 42: 80% Getting block 57 of 213 Reserving size (4338519) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: Getting block 58 of 213 Reserving size (4338519) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: bucket 40: 70% bucket 48: 100% Sorting block of length 1132981 for bucket 48 (Using difference cover) bucket 46: 70% bucket 42: 100% Sorting block of length 4310637 for bucket 42 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3403332 for bucket 29 bucket 49: 100% Sorting block of length 3621555 for bucket 49 (Using difference cover) Getting block 59 of 213 Reserving size (4338519) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 43: 80% bucket 45: 100% Sorting block of length 2458354 for bucket 45 (Using difference cover) Getting block 60 of 213 Reserving size (4338519) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 45: 80% bucket 47: 70% bucket 39: 90% Sorting block time: 00:00:02 Returning block of 2208004 for bucket 29 bucket 55: 10% Getting block 55 of 210 Reserving size (4338519) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 52: 90% bucket 47: 100% Sorting block of length 946096 for bucket 47 (Using difference cover) bucket 34: 90% bucket 31: 100% Sorting block of length 3400836 for bucket 31 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4021311 for bucket 32 bucket 50: 70% bucket 37: 80% bucket 54: 70% bucket 50: 100% Sorting block of length 1254527 for bucket 50 (Using difference cover) bucket 35: 100% Sorting block of length 3705713 for bucket 35 (Using difference cover) Getting block 61 of 213 Reserving size (4338519) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 51: 80% Sorting block time: 00:00:02 Returning block of 1132982 for bucket 48 Sorting block time: 00:00:03 Returning block of 2403801 for bucket 36 Getting block 62 of 213 Reserving size (4338519) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 33: 90% bucket 49: 70% Getting block 63 of 213 Reserving size (4338519) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 36: 100% Sorting block of length 1869321 for bucket 36 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3772823 for bucket 34 bucket 48: 70% bucket 53: 100% Sorting block of length 3886448 for bucket 53 (Using difference cover) bucket 54: 90% Sorting block time: 00:00:03 Returning block of 3587972 for bucket 35 Getting block 64 of 213 Reserving size (4338519) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 32: 90% Sorting block time: 00:00:03 Returning block of 3470009 for bucket 33 bucket 56: 10% Getting block 65 of 213 Reserving size (4338519) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: Sorting block time: 00:00:01 Returning block of 946097 for bucket 47 Getting block 66 of 213 Reserving size (4338519) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: bucket 57: 10% Getting block 67 of 213 Reserving size (4338519) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 41: 70% bucket 44: 100% Sorting block of length 1247440 for bucket 44 (Using difference cover) bucket 59: 10% bucket 60: 10% bucket 51: 100% Sorting block of length 3883160 for bucket 51 (Using difference cover) bucket 58: 10% Sorting block time: 00:00:03 Returning block of 3383925 for bucket 38 bucket 53: 70% bucket 42: 90% Getting block 68 of 213 Reserving size (4338519) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 38: 70% bucket 39: 100% Sorting block of length 3835720 for bucket 39 (Using difference cover) bucket 52: 60% Sorting block time: 00:00:02 Returning block of 1254528 for bucket 50 Sorting block time: 00:00:04 Returning block of 4253236 for bucket 28 bucket 55: 20% Getting block 69 of 213 Reserving size (4338519) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 46: 80% bucket 37: 90% bucket 52: 100% Sorting block of length 4233940 for bucket 52 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2541908 for bucket 44 bucket 40: 80% Getting block 56 of 210 Reserving size (4338519) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 34: 100% Sorting block of length 3509411 for bucket 34 (Using difference cover) bucket 45: 90% Sorting block time: 00:00:04 Returning block of 4071347 for bucket 30 Getting block 70 of 213 Reserving size (4338519) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Sorting block time: 00:00:02 Returning block of 2458355 for bucket 45 bucket 55: 10% Sorting block time: 00:00:04 Returning block of 3872810 for bucket 40 Getting block 57 of 210 Reserving size (4338519) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: Getting block 71 of 213 Reserving size (4338519) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 43: 90% bucket 61: 10% bucket 47: 80% Getting block 72 of 213 Reserving size (4338519) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 62: 10% bucket 63: 10% Sorting block time: 00:00:01 Returning block of 1247441 for bucket 44 Getting block 58 of 210 Reserving size (4338519) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:03 Returning block of 4317753 for bucket 37 Sorting block time: 00:00:01 Returning block of 1869322 for bucket 36 bucket 54: 100% Sorting block of length 4229582 for bucket 54 (Using difference cover) bucket 64: 10% bucket 54: 80% Getting block 59 of 210 Reserving size (4338519) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 56: 20% bucket 51: 90% Getting block 73 of 213 Reserving size (4338519) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 65: 10% bucket 59: 20% bucket 66: 10% bucket 67: 10% bucket 57: 20% Sorting block time: 00:00:03 Returning block of 3621556 for bucket 49 bucket 33: 100% Sorting block of length 3752379 for bucket 33 (Using difference cover) bucket 60: 20% Sorting block time: 00:00:04 Returning block of 3899543 for bucket 46 Getting block 74 of 213 Reserving size (4338519) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 49: 80% bucket 32: 100% Sorting block of length 1153449 for bucket 32 (Using difference cover) Getting block 75 of 213 Reserving size (4338519) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 50: 80% bucket 58: 20% Sorting block time: 00:00:04 Returning block of 4202133 for bucket 41 bucket 68: 10% bucket 48: 80% Getting block 76 of 213 Reserving size (4338519) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 55: 30% Sorting block time: 00:00:03 Returning block of 3400837 for bucket 31 bucket 69: 10% bucket 42: 100% Sorting block of length 2308848 for bucket 42 (Using difference cover) Getting block 60 of 210 Reserving size (4338519) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 70: 10% bucket 38: 80% bucket 41: 80% Sorting block time: 00:00:05 Returning block of 4310638 for bucket 42 Sorting block time: 00:00:04 Returning block of 3705714 for bucket 35 bucket 71: 10% bucket 61: 20% bucket 72: 10% bucket 62: 20% Getting block 77 of 213 Reserving size (4338519) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 53: 80% Getting block 61 of 210 Reserving size (4338519) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: Sorting block time: 00:00:01 Returning block of 1153450 for bucket 32 Getting block 62 of 210 Reserving size (4338519) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 45: 100% Sorting block of length 2428384 for bucket 45 (Using difference cover) bucket 56: 10% bucket 63: 20% Sorting block time: 00:00:03 Returning block of 3886449 for bucket 53 bucket 64: 20% bucket 40: 90% bucket 43: 100% Sorting block of length 4581462 for bucket 43 (Using difference cover) bucket 55: 20% bucket 37: 100% Sorting block of length 2810530 for bucket 37 (Using difference cover) bucket 59: 30% bucket 47: 90% bucket 56: 30% Getting block 78 of 213 Reserving size (4338519) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 73: 10% bucket 65: 20% bucket 66: 20% bucket 52: 70% bucket 57: 30% bucket 57: 10% bucket 67: 20% bucket 46: 90% bucket 60: 30% bucket 58: 10% Sorting block time: 00:00:04 Returning block of 3883161 for bucket 51 bucket 74: 10% bucket 54: 90% bucket 75: 10% bucket 59: 10% bucket 68: 20% bucket 58: 30% bucket 51: 100% Sorting block of length 3627328 for bucket 51 (Using difference cover) Getting block 79 of 213 Reserving size (4338519) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: Sorting block time: 00:00:03 Returning block of 3835721 for bucket 39 Sorting block time: 00:00:03 Returning block of 3509412 for bucket 34 bucket 55: 40% bucket 69: 20% Getting block 63 of 210 Reserving size (4338519) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: Getting block 64 of 210 Reserving size (4338519) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 70: 20% bucket 76: 10% Sorting block time: 00:00:03 Returning block of 4233941 for bucket 52 Sorting block time: 00:00:02 Returning block of 2308849 for bucket 42 bucket 61: 30% bucket 62: 30% Getting block 80 of 213 Reserving size (4338519) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 71: 20% Getting block 65 of 210 Reserving size (4338519) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 72: 20% bucket 77: 10% bucket 49: 90% bucket 59: 40% bucket 64: 30% bucket 63: 30% bucket 50: 90% bucket 60: 10% bucket 56: 40% bucket 78: 10% bucket 73: 20% Sorting block time: 00:00:02 Returning block of 2428385 for bucket 45 bucket 66: 30% bucket 65: 30% bucket 48: 90% bucket 38: 90% Sorting block time: 00:00:03 Returning block of 4229583 for bucket 54 bucket 57: 40% bucket 69: 30% bucket 67: 30% bucket 60: 40% bucket 56: 20% Getting block 66 of 210 Reserving size (4338519) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: Sorting block time: 00:00:03 Returning block of 3752380 for bucket 33 bucket 61: 10% Getting block 81 of 213 Reserving size (4338519) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: Getting block 67 of 210 Reserving size (4338519) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 57: 20% bucket 58: 20% bucket 53: 90% bucket 74: 20% bucket 75: 20% bucket 68: 30% bucket 55: 30% Sorting block time: 00:00:03 Returning block of 2810531 for bucket 37 bucket 58: 40% bucket 55: 50% bucket 79: 10% bucket 40: 100% Sorting block of length 2725146 for bucket 40 (Using difference cover) bucket 41: 90% bucket 47: 100% Sorting block of length 3232498 for bucket 47 (Using difference cover) Getting block 68 of 210 Reserving size (4338519) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 52: 80% bucket 54: 100% Sorting block of length 2273817 for bucket 54 (Using difference cover) bucket 62: 10% bucket 70: 30% bucket 46: 100% Sorting block of length 1926388 for bucket 46 (Using difference cover) bucket 76: 20% bucket 59: 20% bucket 62: 40% bucket 61: 40% bucket 80: 10% bucket 71: 30% bucket 72: 30% bucket 59: 50% bucket 77: 20% bucket 64: 40% bucket 49: 100% Sorting block of length 4234437 for bucket 49 (Using difference cover) bucket 63: 40% bucket 78: 20% bucket 63: 10% bucket 56: 50% bucket 73: 30% bucket 65: 40% bucket 66: 40% bucket 65: 10% bucket 57: 50% bucket 60: 50% bucket 67: 40% bucket 69: 40% Sorting block time: 00:00:03 Returning block of 3627329 for bucket 51 bucket 64: 10% bucket 81: 10% Getting block 69 of 210 Reserving size (4338519) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: Sorting block time: 00:00:04 Returning block of 4581463 for bucket 43 bucket 38: 100% Sorting block of length 4219992 for bucket 38 (Using difference cover) bucket 60: 20% bucket 74: 30% bucket 68: 40% bucket 75: 30% bucket 55: 60% Getting block 70 of 210 Reserving size (4338519) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 58: 50% bucket 79: 20% bucket 57: 30% bucket 56: 30% bucket 70: 40% bucket 61: 20% bucket 55: 40% Sorting block time: 00:00:02 Returning block of 1926389 for bucket 46 bucket 58: 30% bucket 62: 50% Getting block 71 of 210 Reserving size (4338519) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 61: 50% bucket 48: 100% Sorting block of length 2559112 for bucket 48 (Using difference cover) bucket 41: 100% Sorting block of length 3545039 for bucket 41 (Using difference cover) bucket 67: 10% Sorting block time: 00:00:02 Returning block of 2273818 for bucket 54 Sorting block time: 00:00:02 Returning block of 2725147 for bucket 40 bucket 76: 30% Getting block 72 of 210 Reserving size (4338519) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 80: 20% bucket 59: 60% bucket 72: 40% Getting block 73 of 210 Reserving size (4338519) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 71: 40% bucket 52: 90% bucket 64: 50% bucket 50: 100% Sorting block of length 1212371 for bucket 50 (Using difference cover) bucket 53: 100% Sorting block of length 4333335 for bucket 53 (Using difference cover) bucket 59: 30% bucket 63: 50% bucket 77: 30% bucket 78: 30% bucket 56: 60% bucket 65: 50% bucket 73: 40% bucket 66: 50% bucket 57: 60% bucket 60: 60% Sorting block time: 00:00:02 Returning block of 3232499 for bucket 47 bucket 67: 50% bucket 69: 50% bucket 63: 20% Getting block 74 of 210 Reserving size (4338519) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 81: 20% bucket 62: 20% bucket 66: 10% bucket 68: 10% bucket 68: 50% bucket 74: 40% bucket 55: 70% bucket 75: 40% bucket 65: 20% bucket 58: 60% bucket 79: 30% Sorting block time: 00:00:01 Returning block of 1212372 for bucket 50 Getting block 75 of 210 Reserving size (4338519) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 57: 40% bucket 78: 40% bucket 69: 10% bucket 63: 60% bucket 61: 60% bucket 70: 50% bucket 62: 60% bucket 59: 70% bucket 65: 60% bucket 72: 50% bucket 76: 40% bucket 71: 50% bucket 64: 60% bucket 80: 30% bucket 55: 50% bucket 56: 40% bucket 67: 60% bucket 64: 20% bucket 60: 30% bucket 69: 60% bucket 70: 10% Sorting block time: 00:00:02 Returning block of 2559113 for bucket 48 bucket 77: 40% bucket 61: 30% Getting block 76 of 210 Reserving size (4338519) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: Sorting block time: 00:00:03 Returning block of 4234438 for bucket 49 bucket 58: 40% bucket 66: 60% bucket 56: 70% bucket 73: 50% Getting block 77 of 210 Reserving size (4338519) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 60: 70% bucket 57: 70% bucket 59: 40% bucket 74: 10% bucket 52: 100% Sorting block of length 1335638 for bucket 52 (Using difference cover) bucket 71: 10% bucket 72: 10% bucket 68: 60% bucket 74: 50% bucket 61: 70% bucket 75: 50% bucket 55: 80% Sorting block time: 00:00:03 Returning block of 3545040 for bucket 41 Sorting block time: 00:00:04 Returning block of 4219993 for bucket 38 bucket 81: 30% bucket 75: 10% bucket 79: 40% Getting block 78 of 210 Reserving size (4338519) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: Getting block 79 of 210 Reserving size (4338519) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 78: 50% bucket 58: 70% bucket 73: 10% bucket 70: 60% bucket 67: 70% bucket 63: 30% bucket 59: 80% bucket 62: 70% bucket 65: 70% bucket 63: 70% bucket 67: 20% bucket 72: 60% bucket 69: 70% bucket 64: 70% Sorting block time: 00:00:04 Returning block of 4333336 for bucket 53 bucket 71: 60% Sorting block time: 00:00:01 Returning block of 1335639 for bucket 52 bucket 76: 50% Getting block 80 of 210 Reserving size (4338519) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 69: 20% bucket 62: 30% bucket 80: 40% Getting block 81 of 210 Reserving size (4338519) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 65: 30% bucket 55: 60% bucket 60: 40% bucket 77: 50% bucket 66: 20% bucket 68: 20% bucket 76: 10% bucket 66: 70% bucket 57: 50% bucket 73: 60% bucket 56: 80% bucket 57: 80% bucket 60: 80% bucket 61: 80% bucket 56: 50% bucket 68: 70% bucket 64: 30% bucket 74: 60% bucket 75: 60% bucket 55: 90% bucket 61: 40% bucket 81: 40% bucket 79: 50% bucket 78: 60% bucket 58: 50% bucket 70: 20% bucket 77: 10% bucket 62: 80% bucket 67: 80% bucket 59: 90% bucket 58: 80% bucket 59: 50% bucket 70: 70% bucket 74: 20% bucket 75: 20% bucket 72: 70% bucket 69: 80% bucket 65: 80% bucket 63: 80% bucket 64: 80% bucket 71: 70% bucket 73: 20% bucket 78: 10% bucket 76: 60% bucket 81: 10% bucket 80: 50% bucket 65: 40% bucket 79: 10% bucket 66: 80% bucket 77: 60% bucket 63: 40% bucket 80: 10% bucket 73: 70% bucket 61: 90% bucket 56: 90% bucket 60: 90% bucket 57: 90% bucket 76: 20% bucket 72: 20% bucket 68: 80% bucket 69: 30% bucket 78: 70% bucket 74: 70% bucket 75: 70% bucket 71: 20% bucket 60: 50% bucket 55: 100% Sorting block of length 1480679 for bucket 55 (Using difference cover) bucket 57: 60% bucket 62: 40% bucket 69: 90% bucket 79: 60% bucket 67: 30% bucket 55: 70% bucket 81: 50% bucket 62: 90% bucket 59: 100% Sorting block of length 2896845 for bucket 59 (Using difference cover) bucket 66: 30% bucket 67: 90% bucket 68: 30% bucket 64: 40% bucket 58: 90% bucket 72: 80% bucket 61: 50% bucket 64: 90% bucket 65: 90% bucket 70: 80% bucket 73: 30% bucket 63: 90% bucket 71: 80% bucket 56: 60% bucket 74: 30% bucket 80: 60% bucket 76: 70% bucket 58: 60% bucket 75: 30% bucket 77: 20% bucket 66: 90% bucket 80: 20% bucket 77: 70% bucket 61: 100% Sorting block of length 2549648 for bucket 61 (Using difference cover) bucket 56: 100% Sorting block of length 3652761 for bucket 56 (Using difference cover) bucket 73: 80% Sorting block time: 00:00:02 Returning block of 1480680 for bucket 55 bucket 57: 100% Sorting block of length 2644217 for bucket 57 (Using difference cover) Getting block 82 of 213 Reserving size (4338519) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 60: 60% bucket 59: 60% bucket 60: 100% Sorting block of length 2882847 for bucket 60 (Using difference cover) bucket 63: 50% bucket 78: 20% bucket 68: 90% bucket 81: 20% bucket 78: 80% bucket 74: 80% bucket 79: 20% bucket 75: 80% bucket 69: 100% Sorting block of length 2381349 for bucket 69 (Using difference cover) bucket 65: 50% bucket 69: 40% bucket 79: 70% bucket 70: 30% bucket 62: 100% Sorting block of length 2041752 for bucket 62 (Using difference cover) bucket 64: 100% Sorting block of length 3134218 for bucket 64 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2896846 for bucket 59 bucket 67: 100% Sorting block of length 1626954 for bucket 67 (Using difference cover) bucket 80: 70% bucket 81: 60% bucket 72: 90% bucket 72: 30% bucket 73: 40% bucket 57: 70% bucket 58: 100% Sorting block of length 3681876 for bucket 58 (Using difference cover) Getting block 83 of 213 Reserving size (4338519) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 70: 90% bucket 71: 90% bucket 76: 30% bucket 63: 100% Sorting block of length 3759126 for bucket 63 (Using difference cover) bucket 77: 30% bucket 65: 100% Sorting block of length 1735118 for bucket 65 (Using difference cover) bucket 80: 30% bucket 76: 80% bucket 66: 100% Sorting block of length 3020159 for bucket 66 (Using difference cover) bucket 74: 40% bucket 55: 80% bucket 77: 80% bucket 66: 40% bucket 68: 40% bucket 62: 50% bucket 67: 40% bucket 73: 90% bucket 58: 70% bucket 56: 70% bucket 82: 10% bucket 68: 100% Sorting block of length 3892607 for bucket 68 (Using difference cover) bucket 78: 90% bucket 61: 60% bucket 71: 30% Sorting block time: 00:00:02 Returning block of 2549649 for bucket 61 Sorting block time: 00:00:02 Returning block of 2381350 for bucket 69 Getting block 84 of 213 Reserving size (4338519) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 74: 90% bucket 75: 90% Getting block 85 of 213 Reserving size (4338519) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 60: 70% bucket 59: 70% bucket 79: 80% bucket 75: 40% bucket 79: 30% Sorting block time: 00:00:01 Returning block of 1626955 for bucket 67 bucket 64: 50% bucket 80: 40% Sorting block time: 00:00:02 Returning block of 2041753 for bucket 62 Sorting block time: 00:00:02 Returning block of 2644218 for bucket 57 Getting block 86 of 213 Reserving size (4338519) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: Getting block 87 of 213 Reserving size (4338519) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 72: 100% Sorting block of length 3417523 for bucket 72 (Using difference cover) Getting block 88 of 213 Reserving size (4338519) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 80: 80% bucket 81: 30% bucket 83: 10% bucket 73: 50% Sorting block time: 00:00:03 Returning block of 2882848 for bucket 60 bucket 69: 50% bucket 81: 70% Getting block 89 of 213 Reserving size (4338519) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 71: 100% Sorting block of length 4150186 for bucket 71 (Using difference cover) bucket 74: 50% Sorting block time: 00:00:02 Returning block of 1735119 for bucket 65 bucket 70: 100% Sorting block of length 3067890 for bucket 70 (Using difference cover) bucket 63: 60% Sorting block time: 00:00:02 Returning block of 3134219 for bucket 64 bucket 76: 40% bucket 78: 30% Getting block 90 of 213 Reserving size (4338519) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 76: 90% bucket 65: 60% Getting block 91 of 213 Reserving size (4338519) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 77: 40% bucket 78: 100% Sorting block of length 1777893 for bucket 78 (Using difference cover) bucket 77: 90% bucket 73: 100% Sorting block of length 2082918 for bucket 73 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3652762 for bucket 56 bucket 72: 40% bucket 84: 10% bucket 70: 40% bucket 57: 80% bucket 82: 20% Getting block 92 of 213 Reserving size (4338519) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 75: 100% Sorting block of length 2413654 for bucket 75 (Using difference cover) bucket 85: 10% bucket 83: 20% bucket 55: 90% bucket 74: 100% Sorting block of length 3362542 for bucket 74 (Using difference cover) bucket 87: 10% bucket 79: 90% bucket 68: 50% Sorting block time: 00:00:03 Returning block of 3020160 for bucket 66 bucket 58: 80% bucket 56: 80% bucket 80: 90% Getting block 93 of 213 Reserving size (4338519) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 61: 70% Sorting block time: 00:00:03 Returning block of 3681877 for bucket 58 Sorting block time: 00:00:03 Returning block of 3759127 for bucket 63 bucket 71: 40% bucket 88: 10% bucket 86: 10% bucket 76: 100% Sorting block of length 3058170 for bucket 76 (Using difference cover) bucket 79: 40% bucket 73: 60% Getting block 94 of 213 Reserving size (4338519) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: Getting block 95 of 213 Reserving size (4338519) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 60: 80% bucket 59: 80% bucket 66: 50% bucket 80: 50% bucket 64: 60% bucket 77: 100% Sorting block of length 4248492 for bucket 77 (Using difference cover) bucket 89: 10% bucket 84: 20% bucket 67: 50% bucket 62: 60% Sorting block time: 00:00:02 Returning block of 1777894 for bucket 78 bucket 81: 80% bucket 90: 10% Getting block 96 of 213 Reserving size (4338519) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 74: 60% bucket 69: 60% bucket 81: 40% bucket 78: 40% Sorting block time: 00:00:03 Returning block of 3892608 for bucket 68 bucket 92: 10% bucket 91: 10% Sorting block time: 00:00:02 Returning block of 2082919 for bucket 73 bucket 75: 50% bucket 76: 50% Getting block 97 of 213 Reserving size (4338519) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 213 Reserving size (4338519) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 82: 30% Sorting block time: 00:00:03 Returning block of 3417524 for bucket 72 bucket 85: 20% bucket 77: 50% bucket 63: 70% bucket 80: 100% Sorting block of length 2780794 for bucket 80 (Using difference cover) Getting block 99 of 213 Reserving size (4338519) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 79: 100% Sorting block of length 3771895 for bucket 79 (Using difference cover) bucket 57: 90% bucket 83: 30% bucket 87: 20% bucket 94: 10% Sorting block time: 00:00:03 Returning block of 3067891 for bucket 70 bucket 68: 60% bucket 65: 70% bucket 55: 100% Sorting block of length 3972062 for bucket 55 (Using difference cover) bucket 79: 50% Getting block 100 of 213 Reserving size (4338519) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Sorting block time: 00:00:02 Returning block of 2413655 for bucket 75 bucket 86: 20% bucket 72: 50% bucket 88: 20% bucket 93: 10% Getting block 101 of 213 Reserving size (4338519) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 73: 70% bucket 58: 90% bucket 70: 50% bucket 89: 20% bucket 95: 10% bucket 84: 30% bucket 56: 90% Sorting block time: 00:00:03 Returning block of 4150187 for bucket 71 bucket 90: 20% bucket 81: 90% bucket 80: 60% Sorting block time: 00:00:02 Returning block of 3362543 for bucket 74 bucket 99: 10% bucket 96: 10% Sorting block time: 00:00:03 Returning block of 3058171 for bucket 76 bucket 61: 80% Getting block 102 of 213 Reserving size (4338519) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: Getting block 103 of 213 Reserving size (4338519) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: Getting block 104 of 213 Reserving size (4338519) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 71: 50% bucket 74: 70% bucket 92: 20% bucket 59: 90% bucket 91: 20% bucket 69: 70% bucket 66: 60% bucket 60: 90% bucket 98: 10% bucket 85: 30% bucket 64: 70% bucket 97: 10% bucket 78: 50% bucket 82: 40% bucket 83: 40% bucket 86: 30% bucket 75: 60% bucket 57: 100% Sorting block of length 4002170 for bucket 57 (Using difference cover) bucket 81: 50% bucket 87: 30% bucket 94: 20% bucket 76: 60% Sorting block time: 00:00:04 Returning block of 4248493 for bucket 77 bucket 88: 30% bucket 73: 80% bucket 77: 60% bucket 93: 20% bucket 101: 10% bucket 100: 10% bucket 63: 80% Getting block 105 of 213 Reserving size (4338519) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 85: 40% bucket 99: 20% bucket 65: 80% bucket 89: 30% bucket 62: 70% Sorting block time: 00:00:03 Returning block of 2780795 for bucket 80 bucket 84: 40% bucket 67: 60% Getting block 106 of 213 Reserving size (4338519) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 81: 100% Sorting block of length 2790316 for bucket 81 (Using difference cover) bucket 72: 60% bucket 58: 100% Sorting block of length 3077311 for bucket 58 (Using difference cover) bucket 90: 30% bucket 95: 20% bucket 96: 20% bucket 102: 10% bucket 104: 10% bucket 103: 10% bucket 80: 70% bucket 74: 80% Sorting block time: 00:00:04 Returning block of 3771896 for bucket 79 bucket 70: 60% bucket 92: 30% bucket 79: 60% bucket 91: 30% bucket 56: 100% Sorting block of length 497973 for bucket 56 (Using difference cover) Getting block 107 of 213 Reserving size (4338519) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 98: 20% bucket 83: 50% bucket 97: 20% bucket 82: 50% bucket 86: 40% bucket 68: 70% bucket 59: 100% Sorting block of length 1892863 for bucket 59 (Using difference cover) bucket 71: 60% bucket 61: 90% bucket 64: 80% Sorting block time: 00:00:00 Returning block of 497974 for bucket 56 Getting block 82 of 210 Reserving size (4338519) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 88: 40% bucket 87: 40% Sorting block time: 00:00:03 Returning block of 3972063 for bucket 55 bucket 94: 30% bucket 69: 80% bucket 93: 30% bucket 60: 100% Sorting block of length 3636620 for bucket 60 (Using difference cover) bucket 84: 50% bucket 75: 70% bucket 101: 20% bucket 85: 50% bucket 100: 20% Getting block 83 of 210 Reserving size (4338519) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 105: 10% bucket 63: 90% bucket 76: 70% bucket 78: 60% bucket 99: 30% bucket 89: 40% bucket 66: 70% bucket 80: 80% bucket 106: 10% bucket 77: 70% bucket 73: 90% bucket 65: 90% bucket 90: 40% bucket 96: 30% bucket 81: 60% bucket 74: 90% bucket 91: 40% bucket 95: 30% bucket 102: 20% bucket 104: 20% bucket 84: 60% bucket 92: 40% bucket 62: 80% bucket 70: 70% Sorting block time: 00:00:03 Returning block of 2790317 for bucket 81 bucket 103: 20% bucket 107: 10% bucket 82: 60% bucket 97: 30% bucket 71: 70% bucket 98: 30% Getting block 108 of 213 Reserving size (4338519) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 86: 50% bucket 83: 60% Sorting block time: 00:00:02 Returning block of 1892864 for bucket 59 Getting block 84 of 210 Reserving size (4338519) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 72: 70% bucket 67: 70% bucket 79: 70% bucket 88: 50% Sorting block time: 00:00:03 Returning block of 3077312 for bucket 58 bucket 100: 30% Sorting block time: 00:00:04 Returning block of 4002171 for bucket 57 Getting block 85 of 210 Reserving size (4338519) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 93: 40% bucket 64: 90% bucket 94: 40% bucket 85: 60% bucket 87: 50% Getting block 86 of 210 Reserving size (4338519) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: bucket 101: 30% bucket 82: 10% bucket 105: 20% bucket 61: 100% Sorting block of length 3274560 for bucket 61 (Using difference cover) bucket 84: 70% bucket 99: 40% bucket 89: 50% bucket 69: 90% bucket 102: 30% bucket 83: 10% bucket 78: 70% bucket 91: 50% bucket 90: 50% bucket 65: 100% Sorting block of length 3830283 for bucket 65 (Using difference cover) bucket 96: 40% bucket 63: 100% Sorting block of length 3715794 for bucket 63 (Using difference cover) bucket 106: 20% bucket 76: 80% bucket 77: 80% bucket 75: 80% bucket 68: 80% bucket 95: 40% bucket 104: 30% bucket 92: 50% bucket 71: 80% bucket 105: 30% bucket 103: 30% bucket 83: 70% bucket 82: 70% bucket 97: 40% bucket 98: 40% bucket 86: 60% bucket 107: 20% bucket 66: 80% bucket 80: 90% bucket 81: 70% bucket 74: 100% Sorting block of length 1731868 for bucket 74 (Using difference cover) bucket 108: 10% bucket 88: 60% bucket 84: 10% bucket 85: 70% bucket 93: 50% bucket 73: 100% Sorting block of length 3251561 for bucket 73 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3636621 for bucket 60 bucket 79: 80% bucket 100: 40% Getting block 87 of 210 Reserving size (4338519) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 101: 40% bucket 87: 60% bucket 84: 80% bucket 94: 50% bucket 82: 20% bucket 85: 10% bucket 89: 60% bucket 99: 50% bucket 72: 80% bucket 64: 100% Sorting block of length 3928432 for bucket 64 (Using difference cover) bucket 62: 90% bucket 105: 40% bucket 86: 10% bucket 95: 50% bucket 69: 100% Sorting block of length 1158621 for bucket 69 (Using difference cover) bucket 102: 40% bucket 91: 60% bucket 67: 80% bucket 90: 60% bucket 96: 50% bucket 106: 30% bucket 104: 40% bucket 92: 60% bucket 71: 90% bucket 83: 80% bucket 70: 80% bucket 83: 20% Sorting block time: 00:00:01 Returning block of 1731869 for bucket 74 bucket 78: 80% bucket 103: 40% Getting block 88 of 210 Reserving size (4338519) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 86: 70% bucket 97: 50% bucket 98: 50% bucket 77: 90% bucket 82: 80% bucket 107: 30% Sorting block time: 00:00:03 Returning block of 3274561 for bucket 61 bucket 75: 90% bucket 85: 80% bucket 88: 70% Getting block 89 of 210 Reserving size (4338519) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 93: 60% bucket 76: 90% Sorting block time: 00:00:01 Returning block of 1158622 for bucket 69 Getting block 90 of 210 Reserving size (4338519) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 108: 20% bucket 80: 100% Sorting block of length 3977300 for bucket 80 (Using difference cover) bucket 87: 70% bucket 66: 90% bucket 84: 90% bucket 94: 60% bucket 101: 50% bucket 100: 50% bucket 84: 20% bucket 79: 90% bucket 68: 90% bucket 89: 70% bucket 81: 80% bucket 99: 60% bucket 87: 10% bucket 105: 50% bucket 91: 70% Sorting block time: 00:00:04 Returning block of 3830284 for bucket 65 bucket 85: 20% bucket 102: 50% bucket 85: 90% bucket 95: 60% bucket 82: 30% Sorting block time: 00:00:04 Returning block of 3715795 for bucket 63 Getting block 91 of 210 Reserving size (4338519) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: bucket 90: 70% Sorting block time: 00:00:03 Returning block of 3251562 for bucket 73 bucket 86: 20% bucket 96: 60% Getting block 92 of 210 Reserving size (4338519) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Getting block 93 of 210 Reserving size (4338519) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: bucket 83: 90% bucket 106: 40% bucket 104: 50% bucket 72: 90% bucket 62: 100% Sorting block of length 2711598 for bucket 62 (Using difference cover) bucket 87: 80% bucket 92: 70% bucket 88: 10% bucket 82: 90% bucket 103: 50% bucket 86: 80% bucket 98: 60% bucket 97: 60% bucket 71: 100% Sorting block of length 2186319 for bucket 71 (Using difference cover) bucket 88: 80% bucket 83: 30% bucket 107: 40% bucket 89: 10% bucket 77: 100% Sorting block of length 4039153 for bucket 77 (Using difference cover) bucket 67: 90% bucket 78: 90% bucket 84: 100% Sorting block of length 3243946 for bucket 84 (Using difference cover) bucket 93: 70% bucket 70: 90% Sorting block time: 00:00:03 Returning block of 3928433 for bucket 64 bucket 101: 60% bucket 76: 100% Sorting block of length 1905239 for bucket 76 (Using difference cover) bucket 94: 70% bucket 75: 100% Sorting block of length 4131257 for bucket 75 (Using difference cover) Getting block 94 of 210 Reserving size (4338519) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 108: 30% bucket 90: 10% bucket 95: 70% bucket 89: 80% bucket 100: 60% bucket 91: 80% bucket 99: 70% bucket 102: 60% bucket 85: 100% Sorting block of length 1769653 for bucket 85 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3977301 for bucket 80 bucket 90: 80% bucket 105: 60% bucket 79: 100% Sorting block of length 4049666 for bucket 79 (Using difference cover) bucket 85: 30% bucket 84: 30% bucket 83: 100% Sorting block of length 1786959 for bucket 83 (Using difference cover) bucket 82: 40% Getting block 95 of 210 Reserving size (4338519) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 96: 70% bucket 87: 90% bucket 87: 20% bucket 66: 100% Sorting block of length 3604204 for bucket 66 (Using difference cover) bucket 92: 10% bucket 68: 100% Sorting block of length 3360951 for bucket 68 (Using difference cover) bucket 104: 60% bucket 92: 80% bucket 91: 10% bucket 82: 100% Sorting block of length 3855450 for bucket 82 (Using difference cover) bucket 106: 50% bucket 86: 30% bucket 86: 90% bucket 88: 90% bucket 72: 100% Sorting block of length 2812414 for bucket 72 (Using difference cover) bucket 97: 70% bucket 98: 70% bucket 103: 60% Sorting block time: 00:00:03 Returning block of 2711599 for bucket 62 bucket 81: 90% bucket 89: 20% bucket 93: 10% Getting block 96 of 210 Reserving size (4338519) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 88: 20% Sorting block time: 00:00:02 Returning block of 2186320 for bucket 71 Sorting block time: 00:00:02 Returning block of 1905240 for bucket 76 bucket 90: 20% bucket 93: 80% Getting block 97 of 210 Reserving size (4338519) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 107: 50% Getting block 98 of 210 Reserving size (4338519) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 83: 40% bucket 94: 80% bucket 102: 70% Sorting block time: 00:00:01 Returning block of 1769654 for bucket 85 bucket 95: 80% bucket 101: 70% bucket 78: 100% Sorting block of length 3381202 for bucket 78 (Using difference cover) Getting block 109 of 213 Reserving size (4338519) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 89: 90% bucket 91: 90% bucket 96: 80% Sorting block time: 00:00:02 Returning block of 4039154 for bucket 77 Sorting block time: 00:00:01 Returning block of 1786960 for bucket 83 bucket 99: 80% bucket 108: 40% Getting block 110 of 213 Reserving size (4338519) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 100: 70% Getting block 99 of 210 Reserving size (4338519) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 90: 90% bucket 94: 10% bucket 105: 70% bucket 87: 100% Sorting block of length 3283819 for bucket 87 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3243947 for bucket 84 bucket 87: 30% bucket 82: 50% bucket 67: 100% Sorting block of length 3268204 for bucket 67 (Using difference cover) Getting block 111 of 213 Reserving size (4338519) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 84: 40% bucket 97: 80% bucket 104: 70% bucket 92: 90% bucket 96: 10% bucket 70: 100% Sorting block of length 3367630 for bucket 70 (Using difference cover) bucket 86: 100% Sorting block of length 2907390 for bucket 86 (Using difference cover) bucket 91: 20% bucket 85: 40% bucket 88: 100% Sorting block of length 1515302 for bucket 88 (Using difference cover) bucket 102: 80% bucket 106: 60% bucket 95: 10% bucket 103: 70% bucket 98: 80% bucket 90: 30% bucket 92: 20% bucket 86: 40% bucket 81: 100% Sorting block of length 2337509 for bucket 81 (Using difference cover) bucket 109: 10% Sorting block time: 00:00:04 Returning block of 4131258 for bucket 75 bucket 93: 90% bucket 107: 60% bucket 94: 90% bucket 88: 30% Sorting block time: 00:00:03 Returning block of 3360952 for bucket 68 Getting block 100 of 210 Reserving size (4338519) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Sorting block time: 00:00:03 Returning block of 3604205 for bucket 66 bucket 95: 90% bucket 101: 80% bucket 91: 100% Sorting block of length 3949323 for bucket 91 (Using difference cover) bucket 89: 30% Getting block 101 of 210 Reserving size (4338519) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 89: 100% Sorting block of length 3274081 for bucket 89 (Using difference cover) bucket 83: 50% Sorting block time: 00:00:03 Returning block of 4049667 for bucket 79 Getting block 102 of 210 Reserving size (4338519) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 90: 100% Sorting block of length 2387299 for bucket 90 (Using difference cover) bucket 99: 90% bucket 96: 90% bucket 110: 10% Getting block 103 of 210 Reserving size (4338519) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 98: 10% bucket 105: 80% bucket 97: 10% bucket 93: 20% Sorting block time: 00:00:04 Returning block of 2812415 for bucket 72 bucket 100: 80% bucket 108: 50% bucket 97: 90% Getting block 104 of 210 Reserving size (4338519) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Sorting block time: 00:00:02 Returning block of 1515303 for bucket 88 bucket 111: 10% Sorting block time: 00:00:03 Returning block of 3381203 for bucket 78 Getting block 112 of 213 Reserving size (4338519) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: Sorting block time: 00:00:02 Returning block of 3268205 for bucket 67 Sorting block time: 00:00:04 Returning block of 3855451 for bucket 82 Getting block 105 of 210 Reserving size (4338519) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 82: 60% bucket 104: 80% Getting block 106 of 210 Reserving size (4338519) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 92: 100% Sorting block of length 2799007 for bucket 92 (Using difference cover) bucket 102: 90% Getting block 113 of 213 Reserving size (4338519) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 106: 70% bucket 101: 90% bucket 103: 80% bucket 84: 50% bucket 87: 40% bucket 107: 70% bucket 85: 50% bucket 90: 40% Sorting block time: 00:00:01 Returning block of 2337510 for bucket 81 bucket 94: 20% bucket 96: 20% bucket 91: 30% bucket 99: 10% Getting block 107 of 210 Reserving size (4338519) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 98: 90% bucket 105: 90% bucket 101: 10% bucket 94: 100% Sorting block of length 2550560 for bucket 94 (Using difference cover) bucket 109: 20% bucket 93: 100% Sorting block of length 2126570 for bucket 93 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3283820 for bucket 87 bucket 83: 60% bucket 86: 50% bucket 92: 30% bucket 95: 100% Sorting block of length 3778679 for bucket 95 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2907391 for bucket 86 Getting block 114 of 213 Reserving size (4338519) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 95: 20% bucket 89: 40% Getting block 115 of 213 Reserving size (4338519) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 99: 100% Sorting block of length 3425674 for bucket 99 (Using difference cover) bucket 96: 100% Sorting block of length 3899770 for bucket 96 (Using difference cover) bucket 88: 40% bucket 102: 10% Sorting block time: 00:00:03 Returning block of 3367631 for bucket 70 bucket 110: 20% Sorting block time: 00:00:02 Returning block of 2387300 for bucket 90 Getting block 108 of 210 Reserving size (4338519) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 112: 10% Getting block 116 of 213 Reserving size (4338519) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 100: 10% bucket 106: 80% bucket 97: 100% Sorting block of length 3518322 for bucket 97 (Using difference cover) bucket 111: 20% bucket 100: 90% bucket 82: 70% bucket 108: 60% bucket 103: 10% bucket 97: 20% bucket 104: 90% bucket 113: 10% bucket 99: 20% bucket 101: 100% Sorting block of length 3385849 for bucket 101 (Using difference cover) bucket 102: 100% Sorting block of length 3742026 for bucket 102 (Using difference cover) bucket 98: 20% bucket 93: 30% bucket 90: 50% bucket 103: 90% bucket 87: 50% bucket 101: 20% bucket 107: 80% Sorting block time: 00:00:03 Returning block of 3274082 for bucket 89 bucket 114: 10% bucket 105: 100% Sorting block of length 3821550 for bucket 105 (Using difference cover) bucket 98: 100% Sorting block of length 1263555 for bucket 98 (Using difference cover) bucket 104: 10% Getting block 117 of 213 Reserving size (4338519) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 84: 60% bucket 94: 30% bucket 85: 60% Sorting block time: 00:00:03 Returning block of 2799008 for bucket 92 Sorting block time: 00:00:04 Returning block of 3949324 for bucket 91 bucket 105: 10% bucket 106: 10% bucket 109: 30% Getting block 118 of 213 Reserving size (4338519) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: Getting block 119 of 213 Reserving size (4338519) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Sorting block time: 00:00:02 Returning block of 2126571 for bucket 93 bucket 115: 10% bucket 91: 40% bucket 83: 70% Getting block 120 of 213 Reserving size (4338519) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 96: 30% bucket 88: 50% bucket 86: 60% bucket 112: 20% bucket 116: 10% bucket 110: 30% Sorting block time: 00:00:02 Returning block of 2550561 for bucket 94 bucket 107: 10% bucket 92: 40% bucket 111: 30% Getting block 121 of 213 Reserving size (4338519) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 89: 50% bucket 108: 70% bucket 99: 30% bucket 100: 100% Sorting block of length 2294539 for bucket 100 (Using difference cover) bucket 95: 30% Sorting block time: 00:00:02 Returning block of 1263556 for bucket 98 bucket 106: 90% Getting block 122 of 213 Reserving size (4338519) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 113: 20% bucket 117: 10% bucket 104: 100% Sorting block of length 3186822 for bucket 104 (Using difference cover) bucket 87: 60% bucket 103: 100% Sorting block of length 2200162 for bucket 103 (Using difference cover) bucket 103: 20% bucket 108: 10% Sorting block time: 00:00:03 Returning block of 3425675 for bucket 99 Sorting block time: 00:00:03 Returning block of 3899771 for bucket 96 bucket 102: 20% bucket 114: 20% bucket 90: 60% Getting block 123 of 213 Reserving size (4338519) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 100: 20% bucket 82: 80% Getting block 124 of 213 Reserving size (4338519) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 97: 30% bucket 107: 90% bucket 98: 30% Sorting block time: 00:00:03 Returning block of 3778680 for bucket 95 bucket 94: 40% bucket 118: 10% bucket 93: 40% Getting block 125 of 213 Reserving size (4338519) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 119: 10% Sorting block time: 00:00:03 Returning block of 3742027 for bucket 102 bucket 115: 20% Sorting block time: 00:00:03 Returning block of 3385850 for bucket 101 bucket 109: 40% bucket 116: 20% bucket 120: 10% bucket 84: 70% bucket 112: 30% bucket 104: 20% Getting block 126 of 213 Reserving size (4338519) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Getting block 127 of 213 Reserving size (4338519) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 111: 40% Sorting block time: 00:00:03 Returning block of 3518323 for bucket 97 bucket 85: 70% bucket 108: 80% bucket 86: 70% Getting block 128 of 213 Reserving size (4338519) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 121: 10% bucket 110: 40% Sorting block time: 00:00:03 Returning block of 3821551 for bucket 105 bucket 83: 80% bucket 122: 10% bucket 113: 30% Getting block 129 of 213 Reserving size (4338519) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 117: 20% bucket 88: 60% bucket 106: 20% bucket 89: 60% bucket 106: 100% Sorting block of length 846230 for bucket 106 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2294540 for bucket 100 bucket 92: 50% bucket 99: 40% Getting block 130 of 213 Reserving size (4338519) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 101: 30% bucket 114: 30% bucket 91: 50% bucket 123: 10% bucket 96: 40% bucket 124: 10% bucket 127: 10% bucket 107: 20% Sorting block time: 00:00:02 Returning block of 2200163 for bucket 103 bucket 116: 30% Getting block 131 of 213 Reserving size (4338519) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 125: 10% bucket 107: 100% Sorting block of length 3799961 for bucket 107 (Using difference cover) bucket 112: 40% bucket 87: 70% bucket 118: 20% bucket 105: 20% bucket 109: 50% Sorting block time: 00:00:02 Returning block of 3186823 for bucket 104 Sorting block time: 00:00:00 Returning block of 846231 for bucket 106 bucket 119: 20% Getting block 132 of 213 Reserving size (4338519) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 115: 30% Getting block 133 of 213 Reserving size (4338519) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 111: 50% bucket 90: 70% bucket 95: 40% bucket 113: 40% bucket 120: 20% bucket 126: 10% bucket 108: 90% bucket 103: 30% bucket 82: 90% bucket 128: 10% bucket 121: 20% bucket 100: 30% bucket 129: 10% bucket 94: 50% bucket 122: 20% bucket 102: 30% bucket 110: 50% bucket 84: 80% bucket 86: 80% bucket 98: 40% bucket 117: 30% bucket 108: 20% bucket 85: 80% bucket 97: 40% bucket 124: 20% bucket 114: 40% bucket 131: 10% bucket 88: 70% bucket 130: 10% bucket 83: 90% bucket 123: 20% bucket 104: 30% bucket 127: 20% bucket 89: 70% bucket 92: 60% bucket 93: 50% bucket 113: 50% bucket 91: 60% bucket 112: 50% bucket 125: 20% bucket 116: 40% bucket 106: 30% bucket 118: 30% bucket 132: 10% bucket 133: 10% bucket 119: 30% bucket 96: 50% bucket 115: 40% bucket 126: 20% bucket 87: 80% bucket 120: 30% bucket 99: 50% bucket 109: 60% bucket 111: 60% bucket 129: 20% bucket 95: 50% bucket 128: 20% bucket 121: 30% bucket 101: 40% bucket 107: 30% bucket 108: 100% Sorting block of length 3593802 for bucket 108 (Using difference cover) bucket 122: 30% bucket 110: 60% bucket 94: 60% bucket 124: 30% bucket 117: 40% bucket 105: 30% bucket 131: 20% bucket 103: 40% bucket 82: 100% Sorting block of length 3638630 for bucket 82 (Using difference cover) bucket 85: 90% bucket 86: 90% bucket 90: 80% bucket 132: 20% bucket 123: 30% bucket 114: 50% bucket 88: 80% bucket 130: 20% bucket 127: 30% Sorting block time: 00:00:03 Returning block of 3799962 for bucket 107 bucket 112: 60% bucket 84: 90% Getting block 134 of 213 Reserving size (4338519) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 113: 60% bucket 100: 40% bucket 102: 40% bucket 89: 80% bucket 133: 20% bucket 125: 30% bucket 111: 70% bucket 92: 70% bucket 116: 50% bucket 104: 40% bucket 119: 40% bucket 118: 40% bucket 129: 30% bucket 98: 50% bucket 126: 30% bucket 115: 50% bucket 91: 70% bucket 83: 100% Sorting block of length 1467479 for bucket 83 (Using difference cover) bucket 106: 40% bucket 120: 40% bucket 128: 30% bucket 121: 40% bucket 109: 70% bucket 131: 30% bucket 108: 30% bucket 122: 40% bucket 124: 40% bucket 99: 60% bucket 123: 40% bucket 87: 90% bucket 95: 60% bucket 97: 50% bucket 110: 70% bucket 96: 60% bucket 114: 60% bucket 112: 70% bucket 86: 100% Sorting block of length 3186771 for bucket 86 (Using difference cover) bucket 117: 50% bucket 105: 40% bucket 130: 30% bucket 127: 40% bucket 132: 30% bucket 134: 10% bucket 133: 30% bucket 94: 70% bucket 101: 50% bucket 88: 90% bucket 113: 70% bucket 90: 90% bucket 125: 40% bucket 116: 60% bucket 93: 60% bucket 85: 100% Sorting block of length 1561955 for bucket 85 (Using difference cover) bucket 128: 40% bucket 89: 90% bucket 129: 40% bucket 111: 80% bucket 98: 60% Sorting block time: 00:00:02 Returning block of 1467480 for bucket 83 bucket 123: 50% bucket 119: 50% bucket 126: 40% bucket 107: 40% bucket 103: 50% Getting block 109 of 210 Reserving size (4338519) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 115: 60% bucket 118: 50% bucket 131: 40% bucket 121: 50% bucket 84: 100% Sorting block of length 4333416 for bucket 84 (Using difference cover) bucket 117: 60% bucket 100: 50% bucket 120: 50% bucket 122: 50% bucket 92: 80% bucket 124: 50% Sorting block time: 00:00:03 Returning block of 3593803 for bucket 108 bucket 104: 50% Sorting block time: 00:00:03 Returning block of 3638631 for bucket 82 bucket 109: 80% bucket 102: 50% bucket 91: 80% Getting block 110 of 210 Reserving size (4338519) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: Getting block 135 of 213 Reserving size (4338519) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 108: 40% bucket 134: 20% bucket 112: 80% bucket 114: 70% bucket 127: 50% bucket 133: 40% bucket 130: 40% bucket 110: 80% bucket 132: 40% bucket 88: 100% Sorting block of length 1271039 for bucket 88 (Using difference cover) bucket 117: 70% bucket 98: 70% bucket 106: 50% bucket 113: 80% Sorting block time: 00:00:02 Returning block of 1561956 for bucket 85 bucket 129: 50% bucket 125: 50% bucket 128: 50% Getting block 111 of 210 Reserving size (4338519) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 87: 100% Sorting block of length 3281687 for bucket 87 (Using difference cover) bucket 97: 60% bucket 121: 60% bucket 123: 60% bucket 126: 50% bucket 119: 60% bucket 131: 50% bucket 116: 70% bucket 111: 90% bucket 94: 80% bucket 99: 70% bucket 90: 100% Sorting block of length 3544854 for bucket 90 (Using difference cover) bucket 93: 70% bucket 115: 70% bucket 89: 100% Sorting block of length 4073714 for bucket 89 (Using difference cover) bucket 118: 60% bucket 95: 70% bucket 96: 70% bucket 105: 50% bucket 109: 10% bucket 122: 60% bucket 120: 60% Sorting block time: 00:00:03 Returning block of 3186772 for bucket 86 bucket 124: 60% Getting block 112 of 210 Reserving size (4338519) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 107: 50% bucket 132: 50% bucket 134: 30% Sorting block time: 00:00:01 Returning block of 1271040 for bucket 88 bucket 100: 60% Getting block 113 of 210 Reserving size (4338519) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 133: 50% bucket 101: 60% bucket 112: 90% bucket 130: 50% bucket 127: 60% bucket 109: 90% bucket 114: 80% bucket 98: 80% bucket 103: 60% bucket 135: 10% bucket 126: 60% bucket 129: 60% bucket 91: 90% bucket 92: 90% bucket 119: 70% bucket 113: 90% bucket 128: 60% bucket 117: 80% bucket 125: 60% bucket 124: 70% bucket 110: 90% bucket 104: 60% bucket 131: 60% bucket 123: 70% bucket 110: 10% bucket 121: 70% bucket 116: 80% bucket 102: 60% bucket 111: 100% Sorting block of length 4021334 for bucket 111 (Using difference cover) bucket 118: 70% bucket 99: 80% bucket 94: 90% bucket 122: 70% bucket 115: 80% bucket 96: 80% bucket 130: 60% bucket 108: 50% bucket 106: 60% bucket 105: 60% bucket 120: 70% bucket 111: 10% bucket 97: 70% bucket 93: 80% bucket 134: 40% bucket 114: 90% bucket 132: 60% bucket 133: 60% bucket 98: 90% bucket 112: 100% Sorting block of length 1491879 for bucket 112 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4333417 for bucket 84 bucket 127: 70% bucket 129: 70% bucket 109: 20% bucket 100: 70% bucket 126: 70% Getting block 114 of 210 Reserving size (4338519) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: Sorting block time: 00:00:03 Returning block of 3281688 for bucket 87 bucket 121: 80% bucket 135: 20% bucket 113: 100% Sorting block of length 3796110 for bucket 113 (Using difference cover) bucket 128: 70% bucket 109: 100% Sorting block of length 3021337 for bucket 109 (Using difference cover) Getting block 115 of 210 Reserving size (4338519) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: bucket 131: 70% bucket 113: 10% bucket 124: 80% bucket 125: 70% bucket 119: 80% bucket 123: 80% bucket 112: 10% bucket 117: 90% bucket 107: 60% bucket 110: 100% Sorting block of length 3907531 for bucket 110 (Using difference cover) bucket 92: 100% Sorting block of length 2301595 for bucket 92 (Using difference cover) bucket 116: 90% bucket 118: 80% bucket 122: 80% bucket 115: 90% bucket 130: 70% bucket 95: 80% bucket 91: 100% Sorting block of length 3026247 for bucket 91 (Using difference cover) bucket 106: 70% Sorting block time: 00:00:03 Returning block of 3544855 for bucket 90 bucket 131: 80% bucket 103: 70% bucket 134: 50% bucket 99: 90% Sorting block time: 00:00:03 Returning block of 4073715 for bucket 89 bucket 120: 80% bucket 114: 100% Sorting block of length 2386032 for bucket 114 (Using difference cover) Getting block 116 of 210 Reserving size (4338519) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 110: 20% Sorting block time: 00:00:01 Returning block of 1491880 for bucket 112 bucket 133: 70% bucket 101: 70% bucket 132: 70% bucket 126: 80% Getting block 136 of 213 Reserving size (4338519) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 135: 30% Getting block 117 of 210 Reserving size (4338519) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 104: 70% bucket 94: 100% Sorting block of length 4052918 for bucket 94 (Using difference cover) bucket 129: 80% bucket 93: 90% bucket 123: 90% bucket 102: 70% bucket 127: 80% bucket 98: 100% Sorting block of length 2786416 for bucket 98 (Using difference cover) bucket 96: 90% bucket 117: 100% Sorting block of length 3479461 for bucket 117 (Using difference cover) bucket 111: 20% bucket 105: 70% bucket 128: 80% bucket 124: 90% bucket 121: 90% bucket 97: 80% bucket 115: 100% Sorting block of length 4233401 for bucket 115 (Using difference cover) bucket 108: 60% bucket 119: 90% bucket 125: 80% bucket 107: 70% bucket 114: 10% Sorting block time: 00:00:04 Returning block of 4021335 for bucket 111 bucket 100: 80% bucket 118: 90% bucket 109: 30% bucket 122: 90% bucket 116: 100% Sorting block of length 1683610 for bucket 116 (Using difference cover) bucket 106: 80% bucket 130: 80% Getting block 137 of 213 Reserving size (4338519) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 131: 90% bucket 134: 60% bucket 136: 10% Sorting block time: 00:00:03 Returning block of 3021338 for bucket 109 bucket 123: 100% Sorting block of length 3411489 for bucket 123 (Using difference cover) bucket 133: 80% bucket 112: 20% bucket 120: 90% Getting block 138 of 213 Reserving size (4338519) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: Sorting block time: 00:00:02 Returning block of 2301596 for bucket 92 bucket 126: 90% bucket 132: 80% bucket 115: 10% Getting block 118 of 210 Reserving size (4338519) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 129: 90% bucket 113: 20% bucket 135: 40% bucket 99: 100% Sorting block of length 3276536 for bucket 99 (Using difference cover) bucket 127: 90% Sorting block time: 00:00:03 Returning block of 2386033 for bucket 114 Getting block 139 of 213 Reserving size (4338519) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 128: 90% bucket 103: 80% Sorting block time: 00:00:03 Returning block of 3026248 for bucket 91 bucket 124: 100% Sorting block of length 2030684 for bucket 124 (Using difference cover) bucket 104: 80% Getting block 119 of 210 Reserving size (4338519) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 102: 80% bucket 121: 100% Sorting block of length 3723866 for bucket 121 (Using difference cover) bucket 110: 30% bucket 95: 90% bucket 126: 100% Sorting block of length 3699447 for bucket 126 (Using difference cover) bucket 116: 10% bucket 119: 100% Sorting block of length 3245518 for bucket 119 (Using difference cover) bucket 117: 10% bucket 96: 100% Sorting block of length 790365 for bucket 96 (Using difference cover) Sorting block time: 00:00:04 Returning block of 3796111 for bucket 113 Sorting block time: 00:00:03 Returning block of 3907532 for bucket 110 Sorting block time: 00:00:02 Returning block of 2786417 for bucket 98 bucket 101: 80% bucket 122: 100% Sorting block of length 3978972 for bucket 122 (Using difference cover) bucket 93: 100% Sorting block of length 4262389 for bucket 93 (Using difference cover) bucket 131: 100% Sorting block of length 2138193 for bucket 131 (Using difference cover) bucket 118: 100% Sorting block of length 2651064 for bucket 118 (Using difference cover) Getting block 120 of 210 Reserving size (4338519) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: bucket 130: 90% bucket 137: 10% Getting block 140 of 213 Reserving size (4338519) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: Getting block 141 of 213 Reserving size (4338519) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 134: 70% bucket 125: 90% bucket 106: 90% bucket 114: 20% Sorting block time: 00:00:02 Returning block of 1683611 for bucket 116 bucket 133: 90% bucket 136: 20% Getting block 142 of 213 Reserving size (4338519) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 111: 30% bucket 138: 10% bucket 129: 100% Sorting block of length 1940721 for bucket 129 (Using difference cover) bucket 120: 100% Sorting block of length 3315310 for bucket 120 (Using difference cover) bucket 97: 90% bucket 132: 90% Sorting block time: 00:00:01 Returning block of 790366 for bucket 96 Getting block 121 of 210 Reserving size (4338519) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 135: 50% bucket 105: 80% bucket 109: 40% bucket 127: 100% Sorting block of length 3943128 for bucket 127 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3479462 for bucket 117 bucket 128: 100% Sorting block of length 4148079 for bucket 128 (Using difference cover) Getting block 143 of 213 Reserving size (4338519) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 139: 10% Sorting block time: 00:00:02 Returning block of 2030685 for bucket 124 bucket 100: 90% Sorting block time: 00:00:04 Returning block of 4052919 for bucket 94 Getting block 144 of 213 Reserving size (4338519) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 112: 30% Getting block 122 of 210 Reserving size (4338519) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 108: 70% Sorting block time: 00:00:02 Returning block of 2138194 for bucket 131 bucket 107: 80% Getting block 145 of 213 Reserving size (4338519) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 138: 20% Sorting block time: 00:00:03 Returning block of 3411490 for bucket 123 bucket 115: 20% bucket 113: 30% bucket 134: 80% bucket 137: 20% Getting block 146 of 213 Reserving size (4338519) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 140: 10% bucket 130: 100% Sorting block of length 3966808 for bucket 130 (Using difference cover) bucket 118: 10% bucket 125: 100% Sorting block of length 3768147 for bucket 125 (Using difference cover) bucket 133: 100% Sorting block of length 4309806 for bucket 133 (Using difference cover) bucket 141: 10% Sorting block time: 00:00:03 Returning block of 3276537 for bucket 99 Sorting block time: 00:00:04 Returning block of 4233402 for bucket 115 bucket 136: 30% Getting block 123 of 210 Reserving size (4338519) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 102: 90% bucket 142: 10% bucket 103: 90% bucket 110: 40% Sorting block time: 00:00:01 Returning block of 1940722 for bucket 129 Getting block 147 of 213 Reserving size (4338519) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 101: 90% Getting block 148 of 213 Reserving size (4338519) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 104: 90% bucket 132: 100% Sorting block of length 3910041 for bucket 132 (Using difference cover) bucket 116: 20% bucket 119: 10% bucket 135: 60% bucket 95: 100% Sorting block of length 3912757 for bucket 95 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2651065 for bucket 118 bucket 106: 100% Sorting block of length 4192317 for bucket 106 (Using difference cover) Getting block 149 of 213 Reserving size (4338519) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: Sorting block time: 00:00:03 Returning block of 3699448 for bucket 126 bucket 111: 40% bucket 117: 20% bucket 139: 20% bucket 114: 30% Getting block 150 of 213 Reserving size (4338519) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 144: 10% bucket 138: 30% Sorting block time: 00:00:03 Returning block of 3245519 for bucket 119 bucket 143: 10% Getting block 151 of 213 Reserving size (4338519) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 120: 10% Sorting block time: 00:00:04 Returning block of 3723867 for bucket 121 Sorting block time: 00:00:04 Returning block of 4262390 for bucket 93 bucket 145: 10% bucket 137: 30% bucket 134: 90% bucket 142: 20% bucket 105: 90% bucket 97: 100% Sorting block of length 3582742 for bucket 97 (Using difference cover) bucket 109: 50% bucket 140: 20% Getting block 152 of 213 Reserving size (4338519) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Getting block 124 of 210 Reserving size (4338519) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 141: 20% bucket 136: 40% Sorting block time: 00:00:04 Returning block of 3978973 for bucket 122 bucket 146: 10% bucket 121: 10% Sorting block time: 00:00:03 Returning block of 3315311 for bucket 120 Getting block 153 of 213 Reserving size (4338519) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 115: 30% bucket 147: 10% Getting block 154 of 213 Reserving size (4338519) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 112: 40% bucket 148: 10% bucket 122: 10% bucket 135: 70% bucket 100: 100% Sorting block of length 4313416 for bucket 100 (Using difference cover) bucket 113: 40% Sorting block time: 00:00:04 Returning block of 3943129 for bucket 127 bucket 104: 100% Sorting block of length 2555955 for bucket 104 (Using difference cover) Getting block 155 of 213 Reserving size (4338519) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 142: 30% bucket 139: 30% bucket 144: 20% bucket 149: 10% bucket 118: 20% bucket 138: 40% bucket 143: 20% bucket 110: 50% bucket 150: 10% bucket 103: 100% Sorting block of length 3126925 for bucket 103 (Using difference cover) bucket 107: 90% bucket 102: 100% Sorting block of length 3783785 for bucket 102 (Using difference cover) bucket 108: 80% bucket 116: 30% bucket 145: 20% bucket 134: 100% Sorting block of length 2179826 for bucket 134 (Using difference cover) bucket 151: 10% bucket 111: 50% Sorting block time: 00:00:04 Returning block of 4148080 for bucket 128 bucket 101: 100% Sorting block of length 850619 for bucket 101 (Using difference cover) bucket 137: 40% bucket 119: 20% bucket 114: 40% bucket 140: 30% bucket 123: 10% bucket 117: 30% Getting block 156 of 213 Reserving size (4338519) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 152: 10% bucket 141: 30% Sorting block time: 00:00:04 Returning block of 3768148 for bucket 125 bucket 136: 50% Getting block 157 of 213 Reserving size (4338519) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: Sorting block time: 00:00:04 Returning block of 3966809 for bucket 130 Sorting block time: 00:00:04 Returning block of 4309807 for bucket 133 Sorting block time: 00:00:03 Returning block of 3912758 for bucket 95 bucket 153: 10% Getting block 158 of 213 Reserving size (4338519) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: Getting block 159 of 213 Reserving size (4338519) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: Getting block 125 of 210 Reserving size (4338519) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: bucket 135: 80% bucket 147: 20% Sorting block time: 00:00:01 Returning block of 850620 for bucket 101 bucket 109: 60% Getting block 126 of 210 Reserving size (4338519) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Sorting block time: 00:00:03 Returning block of 3910042 for bucket 132 bucket 154: 10% bucket 148: 20% bucket 150: 20% bucket 146: 20% bucket 142: 40% Getting block 160 of 213 Reserving size (4338519) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 155: 10% bucket 143: 30% bucket 139: 40% bucket 151: 20% bucket 138: 50% Sorting block time: 00:00:03 Returning block of 3582743 for bucket 97 bucket 144: 30% bucket 115: 40% bucket 149: 20% bucket 145: 30% Getting block 127 of 210 Reserving size (4338519) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 124: 10% Sorting block time: 00:00:04 Returning block of 4192318 for bucket 106 bucket 113: 50% bucket 112: 50% bucket 122: 20% bucket 114: 50% bucket 120: 20% Getting block 128 of 210 Reserving size (4338519) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: Sorting block time: 00:00:02 Returning block of 2179827 for bucket 134 Sorting block time: 00:00:02 Returning block of 2555956 for bucket 104 bucket 141: 40% Getting block 161 of 213 Reserving size (4338519) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 156: 10% bucket 140: 40% bucket 110: 60% Getting block 129 of 210 Reserving size (4338519) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 136: 60% bucket 105: 100% Sorting block of length 2043576 for bucket 105 (Using difference cover) bucket 157: 10% bucket 137: 50% bucket 152: 20% bucket 116: 40% bucket 153: 20% bucket 158: 10% bucket 118: 30% bucket 108: 90% bucket 121: 20% bucket 135: 90% Sorting block time: 00:00:03 Returning block of 3126926 for bucket 103 bucket 111: 60% bucket 147: 30% bucket 159: 10% Getting block 130 of 210 Reserving size (4338519) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 151: 30% bucket 142: 50% bucket 107: 100% Sorting block of length 2949811 for bucket 107 (Using difference cover) bucket 143: 40% bucket 139: 50% bucket 117: 40% bucket 150: 30% bucket 148: 30% bucket 119: 30% Sorting block time: 00:00:04 Returning block of 4313417 for bucket 100 bucket 154: 20% bucket 138: 60% bucket 155: 20% bucket 160: 10% bucket 146: 30% bucket 136: 70% bucket 144: 40% Getting block 131 of 210 Reserving size (4338519) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 115: 50% bucket 109: 70% bucket 123: 20% bucket 126: 10% bucket 140: 50% bucket 145: 40% bucket 149: 30% Sorting block time: 00:00:04 Returning block of 3783786 for bucket 102 bucket 141: 50% Getting block 132 of 210 Reserving size (4338519) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 139: 60% bucket 156: 20% bucket 125: 10% Sorting block time: 00:00:02 Returning block of 2043577 for bucket 105 bucket 161: 10% bucket 157: 20% bucket 137: 60% bucket 112: 60% bucket 113: 60% bucket 114: 60% Getting block 133 of 210 Reserving size (4338519) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 124: 20% bucket 127: 10% bucket 152: 30% bucket 122: 30% bucket 153: 30% bucket 158: 20% bucket 135: 100% Sorting block of length 3549116 for bucket 135 (Using difference cover) bucket 128: 10% bucket 110: 70% bucket 147: 40% bucket 138: 70% bucket 142: 60% bucket 143: 50% bucket 151: 40% bucket 140: 60% bucket 129: 10% bucket 159: 20% bucket 150: 40% bucket 136: 80% bucket 116: 50% bucket 120: 30% bucket 141: 60% bucket 118: 40% bucket 144: 50% bucket 148: 40% bucket 154: 30% bucket 160: 20% bucket 146: 40% bucket 111: 70% bucket 155: 30% bucket 117: 50% bucket 121: 30% bucket 130: 10% bucket 145: 50% bucket 139: 70% bucket 109: 80% bucket 149: 40% bucket 156: 30% bucket 119: 40% Sorting block time: 00:00:03 Returning block of 2949812 for bucket 107 bucket 157: 30% bucket 108: 100% Sorting block of length 2611640 for bucket 108 (Using difference cover) bucket 115: 60% Getting block 134 of 210 Reserving size (4338519) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 140: 70% bucket 152: 40% bucket 158: 30% bucket 137: 70% bucket 153: 40% bucket 126: 20% bucket 112: 70% bucket 161: 20% bucket 132: 10% bucket 131: 10% bucket 147: 50% bucket 142: 70% bucket 138: 80% bucket 143: 60% bucket 114: 70% bucket 160: 30% bucket 151: 50% bucket 154: 40% bucket 123: 30% bucket 113: 70% bucket 136: 90% bucket 141: 70% bucket 116: 60% bucket 144: 60% bucket 150: 50% bucket 122: 40% bucket 159: 30% bucket 110: 80% bucket 148: 50% bucket 128: 20% bucket 139: 80% bucket 129: 20% bucket 146: 50% bucket 145: 60% bucket 125: 20% bucket 133: 10% Sorting block time: 00:00:03 Returning block of 3549117 for bucket 135 bucket 155: 40% bucket 127: 20% bucket 149: 50% bucket 130: 20% bucket 109: 90% bucket 124: 30% bucket 156: 40% bucket 157: 40% Getting block 162 of 213 Reserving size (4338519) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 140: 80% bucket 118: 50% bucket 117: 60% bucket 111: 80% bucket 137: 80% bucket 121: 40% bucket 120: 40% bucket 158: 40% bucket 136: 100% Sorting block of length 2863251 for bucket 136 (Using difference cover) bucket 152: 50% bucket 153: 50% bucket 142: 80% bucket 138: 90% bucket 115: 70% bucket 160: 40% bucket 144: 70% bucket 161: 30% bucket 143: 70% bucket 147: 60% bucket 119: 50% bucket 151: 60% Sorting block time: 00:00:02 Returning block of 2611641 for bucket 108 bucket 154: 50% bucket 141: 80% Getting block 135 of 210 Reserving size (4338519) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 150: 60% bucket 126: 30% bucket 113: 80% bucket 110: 90% bucket 134: 10% bucket 159: 40% bucket 132: 20% bucket 114: 80% bucket 139: 90% bucket 148: 60% bucket 122: 50% bucket 112: 80% bucket 145: 70% bucket 131: 20% bucket 116: 70% bucket 156: 50% bucket 146: 60% bucket 149: 60% bucket 140: 90% bucket 157: 50% bucket 129: 30% bucket 137: 90% bucket 162: 10% bucket 158: 50% bucket 153: 60% bucket 152: 60% bucket 142: 90% bucket 138: 100% Sorting block of length 2629167 for bucket 138 (Using difference cover) bucket 123: 40% bucket 144: 80% bucket 155: 50% bucket 127: 30% bucket 143: 80% bucket 161: 40% bucket 160: 50% bucket 147: 70% bucket 124: 40% bucket 128: 30% bucket 117: 70% bucket 141: 90% bucket 151: 70% bucket 109: 100% Sorting block of length 4212237 for bucket 109 (Using difference cover) bucket 154: 60% Sorting block time: 00:00:02 Returning block of 2863252 for bucket 136 bucket 118: 60% bucket 139: 100% Sorting block of length 3555696 for bucket 139 (Using difference cover) Getting block 163 of 213 Reserving size (4338519) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 111: 90% bucket 150: 70% bucket 133: 20% bucket 156: 60% bucket 115: 80% bucket 120: 50% bucket 148: 70% bucket 145: 80% bucket 121: 50% bucket 119: 60% bucket 137: 100% Sorting block of length 3000222 for bucket 137 (Using difference cover) bucket 159: 50% bucket 140: 100% Sorting block of length 2010771 for bucket 140 (Using difference cover) bucket 146: 70% bucket 157: 60% bucket 110: 100% Sorting block of length 4086021 for bucket 110 (Using difference cover) bucket 116: 80% bucket 130: 30% bucket 162: 20% bucket 155: 60% bucket 158: 60% bucket 142: 100% Sorting block of length 2391316 for bucket 142 (Using difference cover) bucket 125: 30% bucket 131: 30% bucket 149: 70% bucket 113: 90% bucket 122: 60% bucket 112: 90% bucket 153: 70% bucket 144: 90% bucket 152: 70% bucket 143: 90% bucket 114: 90% bucket 126: 40% bucket 147: 80% bucket 141: 100% bucket 161: 50% Sorting block of length 4301569 for bucket 141 (Using difference cover) bucket 160: 60% Sorting block time: 00:00:02 Returning block of 2629168 for bucket 138 bucket 129: 40% bucket 135: 10% bucket 151: 80% bucket 134: 20% Getting block 164 of 213 Reserving size (4338519) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 154: 70% bucket 163: 10% bucket 132: 30% bucket 150: 80% bucket 156: 70% bucket 123: 50% bucket 115: 90% bucket 117: 80% bucket 127: 40% bucket 148: 80% bucket 157: 70% bucket 111: 100% Sorting block of length 983751 for bucket 111 (Using difference cover) bucket 118: 70% Sorting block time: 00:00:02 Returning block of 2010772 for bucket 140 bucket 145: 90% Getting block 165 of 213 Reserving size (4338519) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 162: 30% bucket 128: 40% bucket 133: 30% bucket 116: 90% bucket 158: 70% bucket 159: 60% bucket 143: 100% Sorting block of length 2377075 for bucket 143 (Using difference cover) bucket 155: 70% bucket 153: 80% bucket 144: 100% Sorting block of length 2493475 for bucket 144 (Using difference cover) bucket 146: 80% bucket 149: 80% bucket 152: 80% bucket 119: 70% bucket 124: 50% bucket 121: 60% Sorting block time: 00:00:03 Returning block of 4212238 for bucket 109 bucket 120: 60% bucket 147: 90% Sorting block time: 00:00:03 Returning block of 3555697 for bucket 139 Sorting block time: 00:00:02 Returning block of 2391317 for bucket 142 Sorting block time: 00:00:02 Returning block of 3000223 for bucket 137 Getting block 136 of 210 Reserving size (4338519) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: Getting block 166 of 213 Reserving size (4338519) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: Sorting block time: 00:00:00 Returning block of 983752 for bucket 111 bucket 113: 100% Sorting block of length 1412802 for bucket 113 (Using difference cover) Getting block 167 of 213 Reserving size (4338519) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: Getting block 168 of 213 Reserving size (4338519) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 160: 70% Getting block 137 of 210 Reserving size (4338519) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 164: 10% bucket 161: 60% bucket 151: 90% bucket 122: 70% bucket 112: 100% Sorting block of length 4078466 for bucket 112 (Using difference cover) bucket 114: 100% Sorting block of length 3502107 for bucket 114 (Using difference cover) bucket 130: 40% bucket 125: 40% bucket 163: 20% bucket 154: 80% bucket 126: 50% bucket 150: 90% bucket 156: 80% bucket 131: 40% bucket 129: 50% bucket 153: 90% bucket 157: 80% bucket 115: 100% Sorting block of length 1200278 for bucket 115 (Using difference cover) bucket 148: 90% bucket 145: 100% Sorting block of length 3195177 for bucket 145 (Using difference cover) bucket 165: 10% bucket 135: 20% bucket 162: 40% bucket 117: 90% bucket 152: 90% bucket 158: 80% bucket 119: 80% bucket 134: 30% bucket 159: 70% Sorting block time: 00:00:04 Returning block of 4086022 for bucket 110 Sorting block time: 00:00:02 Returning block of 1412803 for bucket 113 bucket 155: 80% Getting block 138 of 210 Reserving size (4338519) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: Getting block 139 of 210 Reserving size (4338519) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 118: 80% Sorting block time: 00:00:02 Returning block of 2493476 for bucket 144 bucket 147: 100% Sorting block of length 3670702 for bucket 147 (Using difference cover) bucket 146: 90% Sorting block time: 00:00:02 Returning block of 2377076 for bucket 143 bucket 149: 90% Sorting block time: 00:00:01 Returning block of 1200279 for bucket 115 Getting block 169 of 213 Reserving size (4338519) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: Getting block 170 of 213 Reserving size (4338519) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 168: 10% bucket 151: 100% Sorting block of length 3296705 for bucket 151 (Using difference cover) bucket 167: 10% bucket 166: 10% Getting block 140 of 210 Reserving size (4338519) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 132: 40% bucket 116: 100% Sorting block of length 3768162 for bucket 116 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4301570 for bucket 141 bucket 164: 20% bucket 123: 60% bucket 160: 80% Getting block 171 of 213 Reserving size (4338519) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 161: 70% bucket 127: 50% bucket 150: 100% Sorting block of length 2389031 for bucket 150 (Using difference cover) bucket 163: 30% bucket 128: 50% bucket 154: 90% bucket 136: 10% bucket 156: 90% bucket 153: 100% Sorting block of length 2125943 for bucket 153 (Using difference cover) bucket 121: 70% bucket 157: 90% bucket 122: 80% bucket 133: 40% bucket 137: 10% bucket 148: 100% Sorting block of length 3474877 for bucket 148 (Using difference cover) bucket 130: 50% bucket 124: 60% bucket 162: 50% bucket 126: 60% bucket 165: 20% bucket 152: 100% Sorting block of length 3331198 for bucket 152 (Using difference cover) bucket 158: 90% bucket 129: 60% bucket 120: 70% bucket 159: 80% bucket 155: 90% Sorting block time: 00:00:03 Returning block of 4078467 for bucket 112 bucket 170: 10% Sorting block time: 00:00:03 Returning block of 3502108 for bucket 114 bucket 168: 20% bucket 167: 20% bucket 169: 10% bucket 149: 100% Sorting block of length 3729851 for bucket 149 (Using difference cover) bucket 156: 100% Sorting block of length 3133829 for bucket 156 (Using difference cover) Getting block 141 of 210 Reserving size (4338519) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 166: 20% bucket 146: 100% Sorting block of length 3807323 for bucket 146 (Using difference cover) Getting block 142 of 210 Reserving size (4338519) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 131: 50% bucket 139: 10% bucket 117: 100% Sorting block of length 2093724 for bucket 117 (Using difference cover) bucket 164: 30% bucket 118: 90% Sorting block time: 00:00:03 Returning block of 3195178 for bucket 145 bucket 154: 100% Sorting block of length 3552115 for bucket 154 (Using difference cover) bucket 171: 10% bucket 160: 90% bucket 161: 80% bucket 138: 10% bucket 125: 50% Getting block 172 of 213 Reserving size (4338519) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 163: 40% bucket 119: 90% bucket 128: 60% bucket 134: 40% bucket 140: 10% Sorting block time: 00:00:02 Returning block of 2389032 for bucket 150 bucket 157: 100% Sorting block of length 2433295 for bucket 157 (Using difference cover) bucket 158: 100% Sorting block of length 3744359 for bucket 158 (Using difference cover) bucket 135: 30% Getting block 173 of 213 Reserving size (4338519) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: Sorting block time: 00:00:02 Returning block of 2125944 for bucket 153 bucket 132: 50% Getting block 174 of 213 Reserving size (4338519) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 122: 90% bucket 162: 60% bucket 136: 20% bucket 167: 30% Sorting block time: 00:00:03 Returning block of 3296706 for bucket 151 bucket 170: 20% bucket 127: 60% bucket 159: 90% Getting block 175 of 213 Reserving size (4338519) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 165: 30% Sorting block time: 00:00:03 Returning block of 3670703 for bucket 147 bucket 137: 20% bucket 155: 100% Sorting block of length 3062835 for bucket 155 (Using difference cover) Getting block 176 of 213 Reserving size (4338519) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 123: 70% Sorting block time: 00:00:03 Returning block of 3331199 for bucket 152 bucket 169: 20% Sorting block time: 00:00:04 Returning block of 3768163 for bucket 116 bucket 164: 40% bucket 118: 100% Sorting block of length 4222839 for bucket 118 (Using difference cover) bucket 129: 70% bucket 166: 30% Getting block 177 of 213 Reserving size (4338519) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 168: 30% Sorting block time: 00:00:02 Returning block of 2093725 for bucket 117 bucket 121: 80% Getting block 143 of 210 Reserving size (4338519) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 133: 50% Getting block 144 of 210 Reserving size (4338519) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 171: 20% bucket 163: 50% bucket 130: 60% bucket 160: 100% Sorting block of length 3646154 for bucket 160 (Using difference cover) bucket 128: 70% bucket 142: 10% bucket 161: 90% bucket 126: 70% Sorting block time: 00:00:03 Returning block of 3474878 for bucket 148 bucket 172: 10% bucket 120: 80% bucket 124: 70% bucket 175: 10% Getting block 178 of 213 Reserving size (4338519) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 138: 20% bucket 119: 100% Sorting block of length 3296320 for bucket 119 (Using difference cover) bucket 174: 10% bucket 139: 20% bucket 131: 60% bucket 173: 10% bucket 170: 30% bucket 167: 40% bucket 162: 70% Sorting block time: 00:00:02 Returning block of 2433296 for bucket 157 Sorting block time: 00:00:03 Returning block of 3133830 for bucket 156 Getting block 179 of 213 Reserving size (4338519) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 140: 20% bucket 163: 60% bucket 141: 10% Getting block 180 of 213 Reserving size (4338519) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 125: 60% bucket 159: 100% Sorting block of length 4116329 for bucket 159 (Using difference cover) bucket 122: 100% Sorting block of length 2809922 for bucket 122 (Using difference cover) bucket 165: 40% Sorting block time: 00:00:03 Returning block of 3729852 for bucket 149 Sorting block time: 00:00:03 Returning block of 3807324 for bucket 146 Sorting block time: 00:00:03 Returning block of 3552116 for bucket 154 bucket 176: 10% bucket 166: 40% bucket 169: 30% Getting block 181 of 213 Reserving size (4338519) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: Getting block 182 of 213 Reserving size (4338519) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: Getting block 183 of 213 Reserving size (4338519) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 136: 30% bucket 161: 100% Sorting block of length 3593207 for bucket 161 (Using difference cover) bucket 137: 30% bucket 134: 50% bucket 177: 10% bucket 164: 50% bucket 168: 40% bucket 132: 60% bucket 171: 30% Sorting block time: 00:00:03 Returning block of 3744360 for bucket 158 bucket 135: 40% Getting block 184 of 213 Reserving size (4338519) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 144: 10% bucket 127: 70% bucket 175: 20% bucket 129: 80% bucket 138: 30% bucket 162: 80% bucket 172: 20% bucket 178: 10% bucket 143: 10% bucket 174: 20% bucket 167: 50% bucket 173: 20% Sorting block time: 00:00:02 Returning block of 3062836 for bucket 155 bucket 170: 40% bucket 142: 20% bucket 123: 80% bucket 133: 60% Getting block 185 of 213 Reserving size (4338519) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 179: 10% bucket 180: 10% Sorting block time: 00:00:03 Returning block of 4222840 for bucket 118 bucket 163: 70% bucket 128: 80% bucket 121: 90% bucket 130: 70% Getting block 145 of 210 Reserving size (4338519) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 183: 10% bucket 176: 20% bucket 126: 80% bucket 169: 40% bucket 166: 50% bucket 124: 80% bucket 165: 50% bucket 164: 60% bucket 181: 10% Sorting block time: 00:00:03 Returning block of 3646155 for bucket 160 Sorting block time: 00:00:02 Returning block of 2809923 for bucket 122 bucket 171: 40% bucket 177: 20% bucket 182: 10% bucket 120: 90% Sorting block time: 00:00:02 Returning block of 3296321 for bucket 119 bucket 139: 30% Getting block 146 of 210 Reserving size (4338519) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: Getting block 186 of 213 Reserving size (4338519) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 168: 50% Getting block 147 of 210 Reserving size (4338519) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 141: 20% bucket 140: 30% bucket 184: 10% bucket 162: 90% bucket 131: 70% bucket 136: 40% bucket 175: 30% bucket 125: 70% bucket 178: 20% bucket 137: 40% bucket 179: 20% bucket 174: 30% bucket 167: 60% bucket 170: 50% bucket 134: 60% bucket 143: 20% bucket 177: 30% bucket 173: 30% bucket 164: 70% bucket 185: 10% bucket 180: 20% bucket 127: 80% bucket 172: 30% bucket 176: 30% bucket 138: 40% bucket 129: 90% Sorting block time: 00:00:03 Returning block of 3593208 for bucket 161 bucket 144: 20% bucket 163: 80% Sorting block time: 00:00:04 Returning block of 4116330 for bucket 159 bucket 135: 50% Getting block 187 of 213 Reserving size (4338519) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 183: 20% bucket 142: 30% bucket 166: 60% Getting block 188 of 213 Reserving size (4338519) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 133: 70% bucket 171: 50% bucket 132: 70% bucket 165: 60% bucket 147: 10% bucket 169: 50% bucket 123: 90% bucket 186: 10% bucket 182: 20% bucket 181: 20% bucket 184: 20% bucket 180: 30% bucket 162: 100% Sorting block of length 1757330 for bucket 162 (Using difference cover) bucket 130: 80% bucket 145: 10% bucket 167: 70% bucket 178: 30% bucket 175: 40% bucket 168: 60% bucket 126: 90% bucket 146: 10% bucket 179: 30% bucket 121: 100% Sorting block of length 3847057 for bucket 121 (Using difference cover) bucket 177: 40% bucket 174: 40% bucket 141: 30% bucket 170: 60% bucket 124: 90% bucket 136: 50% bucket 139: 40% bucket 128: 90% bucket 185: 20% bucket 166: 70% bucket 176: 40% bucket 140: 40% bucket 163: 90% bucket 173: 40% bucket 125: 80% bucket 164: 80% bucket 184: 30% bucket 120: 100% Sorting block of length 2884204 for bucket 120 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1757331 for bucket 162 bucket 172: 40% bucket 181: 30% bucket 137: 50% bucket 138: 50% bucket 183: 30% Getting block 189 of 213 Reserving size (4338519) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 134: 70% bucket 188: 10% bucket 186: 20% bucket 187: 10% bucket 171: 60% bucket 143: 30% bucket 131: 80% bucket 129: 100% Sorting block of length 3688088 for bucket 129 (Using difference cover) bucket 144: 30% bucket 182: 30% bucket 170: 70% bucket 165: 70% bucket 180: 40% bucket 142: 40% bucket 169: 60% bucket 167: 80% bucket 179: 40% bucket 145: 20% bucket 175: 50% bucket 127: 90% bucket 174: 50% bucket 178: 40% bucket 168: 70% bucket 177: 50% bucket 184: 40% bucket 147: 20% bucket 182: 40% bucket 166: 80% bucket 176: 50% bucket 163: 100% Sorting block of length 4091775 for bucket 163 (Using difference cover) bucket 185: 30% bucket 170: 80% bucket 188: 20% bucket 133: 80% bucket 139: 50% bucket 189: 10% bucket 180: 50% bucket 136: 60% bucket 183: 40% bucket 173: 50% bucket 186: 30% bucket 171: 70% bucket 146: 20% bucket 135: 60% bucket 181: 40% bucket 126: 100% Sorting block of length 3436426 for bucket 126 (Using difference cover) bucket 123: 100% Sorting block of length 2173125 for bucket 123 (Using difference cover) bucket 172: 50% bucket 132: 80% bucket 164: 90% bucket 169: 70% bucket 130: 90% bucket 140: 50% bucket 165: 80% Sorting block time: 00:00:03 Returning block of 3847058 for bucket 121 bucket 187: 20% bucket 137: 60% bucket 167: 90% bucket 179: 50% bucket 182: 50% Getting block 148 of 210 Reserving size (4338519) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 170: 90% bucket 175: 60% bucket 142: 50% bucket 128: 100% Sorting block of length 2731968 for bucket 128 (Using difference cover) bucket 125: 90% bucket 138: 60% bucket 131: 90% bucket 144: 40% bucket 174: 60% Sorting block time: 00:00:03 Returning block of 2884205 for bucket 120 bucket 141: 40% bucket 178: 50% bucket 177: 60% Getting block 149 of 210 Reserving size (4338519) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 143: 40% bucket 184: 50% bucket 168: 80% bucket 124: 100% Sorting block of length 3641617 for bucket 124 (Using difference cover) bucket 145: 30% bucket 134: 80% bucket 166: 90% bucket 188: 30% bucket 176: 60% Sorting block time: 00:00:03 Returning block of 3688089 for bucket 129 bucket 189: 20% bucket 147: 30% bucket 139: 60% Getting block 150 of 210 Reserving size (4338519) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 180: 60% bucket 186: 40% bucket 181: 50% bucket 185: 40% bucket 173: 60% bucket 171: 80% bucket 183: 50% bucket 169: 80% bucket 140: 60% Sorting block time: 00:00:01 Returning block of 2173126 for bucket 123 bucket 172: 60% Getting block 151 of 210 Reserving size (4338519) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 165: 90% bucket 177: 70% bucket 164: 100% Sorting block of length 2211038 for bucket 164 (Using difference cover) bucket 174: 70% bucket 167: 100% Sorting block of length 3544300 for bucket 167 (Using difference cover) bucket 179: 60% bucket 170: 100% Sorting block of length 2624447 for bucket 170 (Using difference cover) bucket 136: 70% bucket 127: 100% Sorting block of length 2706045 for bucket 127 (Using difference cover) bucket 182: 60% bucket 175: 70% bucket 187: 30% bucket 146: 30% bucket 184: 60% Sorting block time: 00:00:03 Returning block of 4091776 for bucket 163 bucket 180: 70% bucket 181: 60% Getting block 190 of 213 Reserving size (4338519) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 178: 60% bucket 168: 90% bucket 133: 90% bucket 130: 100% Sorting block of length 2352152 for bucket 130 (Using difference cover) bucket 166: 100% Sorting block of length 3803432 for bucket 166 (Using difference cover) bucket 188: 40% bucket 176: 70% bucket 189: 30% Sorting block time: 00:00:03 Returning block of 2731969 for bucket 128 bucket 137: 70% bucket 142: 60% Getting block 152 of 210 Reserving size (4338519) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 186: 50% bucket 138: 70% bucket 135: 70% Sorting block time: 00:00:03 Returning block of 3436427 for bucket 126 bucket 144: 50% bucket 145: 40% bucket 171: 90% bucket 149: 10% bucket 143: 50% Getting block 153 of 210 Reserving size (4338519) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 173: 70% bucket 185: 50% bucket 169: 90% bucket 147: 40% bucket 183: 60% bucket 182: 70% bucket 174: 80% bucket 150: 10% bucket 148: 10% bucket 179: 70% bucket 131: 100% Sorting block of length 3597640 for bucket 131 (Using difference cover) bucket 177: 80% bucket 165: 100% Sorting block of length 3810700 for bucket 165 (Using difference cover) bucket 172: 70% bucket 132: 90% bucket 180: 80% Sorting block time: 00:00:02 Returning block of 2211039 for bucket 164 bucket 139: 70% bucket 175: 80% Sorting block time: 00:00:02 Returning block of 2352153 for bucket 130 Getting block 191 of 213 Reserving size (4338519) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 136: 80% Getting block 154 of 210 Reserving size (4338519) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 151: 10% bucket 125: 100% Sorting block of length 3132241 for bucket 125 (Using difference cover) bucket 184: 70% bucket 140: 70% bucket 168: 100% Sorting block of length 4230566 for bucket 168 (Using difference cover) bucket 190: 10% Sorting block time: 00:00:03 Returning block of 3641618 for bucket 124 bucket 187: 40% Sorting block time: 00:00:02 Returning block of 2706046 for bucket 127 Sorting block time: 00:00:02 Returning block of 2624448 for bucket 170 Getting block 155 of 210 Reserving size (4338519) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 134: 90% Getting block 156 of 210 Reserving size (4338519) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 182: 80% bucket 189: 40% Getting block 192 of 213 Reserving size (4338519) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 178: 70% bucket 176: 80% bucket 183: 70% bucket 181: 70% bucket 146: 40% bucket 141: 50% bucket 186: 60% bucket 188: 50% bucket 171: 100% Sorting block of length 3152347 for bucket 171 (Using difference cover) bucket 169: 100% Sorting block of length 3589198 for bucket 169 (Using difference cover) bucket 173: 80% bucket 185: 60% Sorting block time: 00:00:03 Returning block of 3544301 for bucket 167 bucket 174: 90% Getting block 193 of 213 Reserving size (4338519) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 179: 80% bucket 133: 100% Sorting block of length 1977925 for bucket 133 (Using difference cover) bucket 177: 90% bucket 152: 10% bucket 172: 80% bucket 142: 70% bucket 180: 90% bucket 191: 10% bucket 150: 20% bucket 175: 90% bucket 137: 80% bucket 184: 80% bucket 147: 50% bucket 138: 80% bucket 143: 60% bucket 190: 20% bucket 187: 50% bucket 192: 10% Sorting block time: 00:00:04 Returning block of 3803433 for bucket 166 bucket 189: 50% bucket 182: 90% bucket 178: 80% bucket 181: 80% bucket 148: 20% bucket 176: 90% bucket 183: 80% bucket 135: 80% Getting block 194 of 213 Reserving size (4338519) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 139: 80% bucket 145: 50% bucket 186: 70% bucket 144: 60% bucket 188: 60% Sorting block time: 00:00:02 Returning block of 3132242 for bucket 125 bucket 185: 70% bucket 140: 80% bucket 149: 20% Getting block 157 of 210 Reserving size (4338519) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 173: 90% bucket 146: 50% Sorting block time: 00:00:04 Returning block of 3810701 for bucket 165 bucket 132: 100% Sorting block of length 4118255 for bucket 132 (Using difference cover) bucket 174: 100% Sorting block of length 4069524 for bucket 174 (Using difference cover) bucket 193: 10% bucket 179: 90% Sorting block time: 00:00:04 Returning block of 3597641 for bucket 131 Getting block 195 of 213 Reserving size (4338519) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 153: 10% bucket 151: 20% bucket 136: 90% Getting block 158 of 210 Reserving size (4338519) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: Sorting block time: 00:00:02 Returning block of 1977926 for bucket 133 bucket 177: 100% Sorting block of length 3229106 for bucket 177 (Using difference cover) bucket 180: 100% Sorting block of length 3421559 for bucket 180 (Using difference cover) bucket 172: 90% bucket 191: 20% Getting block 159 of 210 Reserving size (4338519) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 175: 100% Sorting block of length 4219103 for bucket 175 (Using difference cover) bucket 141: 60% bucket 184: 90% bucket 134: 100% Sorting block of length 2879289 for bucket 134 (Using difference cover) bucket 190: 30% Sorting block time: 00:00:03 Returning block of 4230567 for bucket 168 bucket 154: 10% Sorting block time: 00:00:02 Returning block of 3152348 for bucket 171 Getting block 196 of 213 Reserving size (4338519) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 192: 20% Getting block 197 of 213 Reserving size (4338519) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: Sorting block time: 00:00:03 Returning block of 3589199 for bucket 169 bucket 150: 30% bucket 189: 60% bucket 152: 20% bucket 182: 100% Sorting block of length 3517799 for bucket 182 (Using difference cover) bucket 178: 90% bucket 181: 90% bucket 187: 60% bucket 156: 10% Getting block 198 of 213 Reserving size (4338519) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 183: 90% bucket 194: 10% bucket 155: 10% bucket 176: 100% Sorting block of length 1915932 for bucket 176 (Using difference cover) bucket 142: 80% bucket 186: 80% bucket 188: 70% bucket 185: 80% bucket 138: 90% bucket 173: 100% Sorting block of length 987385 for bucket 173 (Using difference cover) bucket 143: 70% bucket 193: 20% bucket 137: 90% bucket 195: 10% bucket 179: 100% Sorting block of length 2929018 for bucket 179 (Using difference cover) bucket 140: 90% bucket 191: 30% bucket 172: 100% Sorting block of length 3481881 for bucket 172 (Using difference cover) bucket 148: 30% bucket 145: 60% bucket 147: 60% bucket 190: 40% bucket 139: 90% bucket 184: 100% Sorting block of length 3114918 for bucket 184 (Using difference cover) Sorting block time: 00:00:01 Returning block of 987386 for bucket 173 Getting block 199 of 213 Reserving size (4338519) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 196: 10% bucket 135: 90% bucket 146: 60% bucket 197: 10% bucket 192: 30% bucket 144: 70% bucket 189: 70% bucket 181: 100% Sorting block of length 2863918 for bucket 181 (Using difference cover) bucket 178: 100% Sorting block of length 4007875 for bucket 178 (Using difference cover) bucket 183: 100% Sorting block of length 1988534 for bucket 183 (Using difference cover) bucket 198: 10% bucket 194: 20% bucket 159: 10% bucket 154: 20% bucket 186: 90% Sorting block time: 00:00:02 Returning block of 1915933 for bucket 176 bucket 185: 90% bucket 188: 80% bucket 187: 70% Getting block 200 of 213 Reserving size (4338519) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: Sorting block time: 00:00:03 Returning block of 2879290 for bucket 134 bucket 150: 40% bucket 153: 20% Getting block 160 of 210 Reserving size (4338519) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 193: 30% bucket 136: 100% Sorting block of length 2665846 for bucket 136 (Using difference cover) Sorting block time: 00:00:03 Returning block of 3229107 for bucket 177 bucket 151: 30% Sorting block time: 00:00:03 Returning block of 3421560 for bucket 180 Getting block 201 of 213 Reserving size (4338519) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Sorting block time: 00:00:03 Returning block of 4118256 for bucket 132 bucket 195: 20% Getting block 202 of 213 Reserving size (4338519) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 158: 10% bucket 149: 30% Sorting block time: 00:00:03 Returning block of 4069525 for bucket 174 bucket 191: 40% bucket 157: 10% Getting block 161 of 210 Reserving size (4338519) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 155: 20% Getting block 203 of 213 Reserving size (4338519) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 137: 100% Sorting block of length 4318754 for bucket 137 (Using difference cover) bucket 190: 50% bucket 198: 20% Sorting block time: 00:00:03 Returning block of 3517800 for bucket 182 bucket 142: 90% bucket 140: 100% Sorting block of length 3639901 for bucket 140 (Using difference cover) bucket 138: 100% Sorting block of length 2826660 for bucket 138 (Using difference cover) bucket 199: 10% bucket 143: 80% bucket 196: 20% Getting block 204 of 213 Reserving size (4338519) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 156: 20% bucket 197: 20% bucket 192: 40% bucket 141: 70% Sorting block time: 00:00:04 Returning block of 4219104 for bucket 175 bucket 189: 80% Sorting block time: 00:00:03 Returning block of 2929019 for bucket 179 Getting block 205 of 213 Reserving size (4338519) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:02 Returning block of 1988535 for bucket 183 bucket 194: 30% Getting block 206 of 213 Reserving size (4338519) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: Getting block 207 of 213 Reserving size (4338519) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 145: 70% bucket 148: 40% bucket 186: 100% Sorting block of length 4139926 for bucket 186 (Using difference cover) bucket 188: 90% bucket 200: 10% bucket 185: 100% Sorting block of length 3588016 for bucket 185 (Using difference cover) bucket 187: 80% bucket 193: 40% bucket 152: 30% bucket 139: 100% Sorting block of length 3269890 for bucket 139 (Using difference cover) bucket 135: 100% Sorting block of length 4329281 for bucket 135 (Using difference cover) bucket 201: 10% bucket 195: 30% bucket 146: 70% bucket 202: 10% bucket 147: 70% Sorting block time: 00:00:03 Returning block of 3114919 for bucket 184 bucket 144: 80% Sorting block time: 00:00:03 Returning block of 2863919 for bucket 181 Sorting block time: 00:00:03 Returning block of 3481882 for bucket 172 bucket 198: 30% Getting block 208 of 213 Reserving size (4338519) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 191: 50% Getting block 209 of 213 Reserving size (4338519) for bucket 209 Calculating Z arrays for bucket 209 Entering block accumulator loop for bucket 209: bucket 154: 30% Getting block 210 of 213 Reserving size (4338519) for bucket 210 Calculating Z arrays for bucket 210 Entering block accumulator loop for bucket 210: bucket 203: 10% bucket 190: 60% bucket 150: 50% bucket 159: 20% bucket 196: 30% bucket 199: 20% Sorting block time: 00:00:02 Returning block of 2665847 for bucket 136 bucket 204: 10% bucket 197: 30% bucket 192: 50% bucket 189: 90% Getting block 162 of 210 Reserving size (4338519) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 158: 20% bucket 205: 10% bucket 206: 10% bucket 194: 40% bucket 207: 10% bucket 153: 30% bucket 151: 40% Sorting block time: 00:00:04 Returning block of 4007876 for bucket 178 bucket 160: 10% bucket 200: 20% bucket 188: 100% Sorting block of length 2121492 for bucket 188 (Using difference cover) Getting block 211 of 213 Reserving size (4338519) for bucket 211 Calculating Z arrays for bucket 211 Entering block accumulator loop for bucket 211: bucket 142: 100% Sorting block of length 3696206 for bucket 142 (Using difference cover) bucket 193: 50% bucket 143: 90% bucket 161: 10% bucket 149: 40% bucket 187: 90% bucket 157: 20% bucket 198: 40% bucket 195: 40% bucket 201: 20% bucket 202: 20% bucket 208: 10% Sorting block time: 00:00:03 Returning block of 2826661 for bucket 138 bucket 209: 10% bucket 145: 80% bucket 191: 60% bucket 210: 10% bucket 155: 30% bucket 203: 20% Getting block 163 of 210 Reserving size (4338519) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 148: 50% bucket 156: 30% bucket 190: 70% bucket 141: 80% bucket 196: 40% bucket 144: 90% bucket 199: 30% bucket 146: 80% bucket 204: 20% bucket 197: 40% bucket 192: 60% bucket 147: 80% bucket 152: 40% bucket 205: 20% Sorting block time: 00:00:03 Returning block of 3588017 for bucket 185 bucket 206: 20% Sorting block time: 00:00:03 Returning block of 3639902 for bucket 140 bucket 207: 20% bucket 194: 50% bucket 189: 100% Sorting block of length 2932921 for bucket 189 (Using difference cover) Sorting block time: 00:00:04 Returning block of 4318755 for bucket 137 Getting block 164 of 210 Reserving size (4338519) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 200: 30% Getting block 212 of 213 Reserving size (4338519) for bucket 212 Calculating Z arrays for bucket 212 Entering block accumulator loop for bucket 212: bucket 211: 10% Getting block 165 of 210 Reserving size (4338519) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 193: 60% Sorting block time: 00:00:03 Returning block of 3269891 for bucket 139 Sorting block time: 00:00:04 Returning block of 4139927 for bucket 186 bucket 150: 60% Sorting block time: 00:00:02 Returning block of 2121493 for bucket 188 Getting block 166 of 210 Reserving size (4338519) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 195: 50% bucket 201: 30% Getting block 213 of 213 Reserving size (4338519) for bucket 213 Calculating Z arrays for bucket 213 Entering block accumulator loop for bucket 213: bucket 198: 50% bucket 154: 40% bucket 187: 100% Sorting block of length 4106425 for bucket 187 (Using difference cover) bucket 202: 30% Sorting block time: 00:00:03 Returning block of 4329282 for bucket 135 bucket 162: 10% bucket 158: 30% bucket 209: 20% bucket 210: 20% bucket 203: 30% bucket 191: 70% Getting block 167 of 210 Reserving size (4338519) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 208: 20% bucket 205: 30% bucket 190: 80% bucket 159: 30% bucket 160: 20% bucket 196: 50% bucket 204: 30% bucket 153: 40% bucket 199: 40% bucket 197: 50% bucket 192: 70% bucket 206: 30% bucket 143: 100% Sorting block of length 4191375 for bucket 143 (Using difference cover) bucket 144: 100% Sorting block of length 4218216 for bucket 144 (Using difference cover) bucket 161: 20% bucket 151: 50% bucket 207: 30% bucket 213: 10% bucket 194: 60% bucket 145: 90% bucket 200: 40% bucket 212: 10% bucket 193: 70% bucket 163: 10% bucket 211: 20% bucket 156: 40% Sorting block time: 00:00:03 Returning block of 3696207 for bucket 142 bucket 149: 50% bucket 147: 90% Getting block 168 of 210 Reserving size (4338519) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 195: 60% bucket 201: 40% bucket 157: 30% bucket 146: 90% bucket 190: 90% bucket 202: 40% bucket 198: 60% bucket 209: 30% bucket 205: 40% bucket 210: 30% bucket 203: 40% bucket 148: 60% bucket 191: 80% bucket 155: 40% bucket 208: 30% bucket 196: 60% bucket 167: 10% bucket 164: 10% bucket 141: 90% bucket 150: 70% bucket 213: 20% Sorting block time: 00:00:02 Returning block of 2932922 for bucket 189 bucket 204: 40% bucket 165: 10% bucket 199: 50% bucket 152: 50% bucket 166: 10% bucket 162: 20% bucket 197: 60% bucket 192: 80% bucket 158: 40% bucket 206: 40% bucket 207: 40% bucket 194: 70% bucket 212: 20% bucket 200: 50% bucket 211: 30% bucket 193: 80% bucket 201: 50% bucket 154: 50% bucket 163: 20% bucket 195: 70% bucket 213: 30% bucket 190: 100% Sorting block of length 2316554 for bucket 190 (Using difference cover) bucket 196: 70% bucket 205: 50% bucket 209: 40% bucket 202: 50% Sorting block time: 00:00:03 Returning block of 4106426 for bucket 187 bucket 198: 70% bucket 210: 40% bucket 203: 50% bucket 208: 40% bucket 159: 40% bucket 191: 90% bucket 145: 100% Sorting block of length 3468740 for bucket 145 (Using difference cover) bucket 153: 50% bucket 160: 30% bucket 192: 90% bucket 204: 50% bucket 167: 20% bucket 168: 10% bucket 146: 100% Sorting block of length 4245455 for bucket 146 (Using difference cover) bucket 147: 100% Sorting block of length 2771851 for bucket 147 (Using difference cover) bucket 199: 60% bucket 161: 30% bucket 197: 70% bucket 206: 50% bucket 165: 20% bucket 151: 60% bucket 156: 50% bucket 207: 50% bucket 149: 60% Sorting block time: 00:00:03 Returning block of 4191376 for bucket 143 bucket 164: 20% bucket 157: 40% bucket 200: 60% bucket 212: 30% bucket 213: 40% bucket 194: 80% bucket 211: 40% bucket 203: 60% bucket 193: 90% Getting block 169 of 210 Reserving size (4338519) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: Sorting block time: 00:00:04 Returning block of 4218217 for bucket 144 bucket 201: 60% bucket 150: 80% bucket 158: 50% bucket 148: 70% bucket 166: 20% bucket 155: 50% Getting block 170 of 210 Reserving size (4338519) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 195: 80% bucket 162: 30% Sorting block time: 00:00:02 Returning block of 2316555 for bucket 190 bucket 152: 60% bucket 141: 100% Sorting block of length 2805698 for bucket 141 (Using difference cover) bucket 196: 80% bucket 202: 60% bucket 209: 50% bucket 205: 60% bucket 210: 50% bucket 213: 50% bucket 206: 60% bucket 199: 70% bucket 208: 50% bucket 198: 80% bucket 191: 100% Sorting block of length 3048801 for bucket 191 (Using difference cover) bucket 194: 90% bucket 192: 100% Sorting block of length 3904062 for bucket 192 (Using difference cover) bucket 204: 60% bucket 203: 70% bucket 197: 80% bucket 163: 30% bucket 207: 60% bucket 213: 60% bucket 200: 70% bucket 212: 40% bucket 205: 70% bucket 211: 50% bucket 209: 60% bucket 154: 60% bucket 193: 100% Sorting block of length 3374761 for bucket 193 (Using difference cover) bucket 167: 30% bucket 168: 20% bucket 201: 70% Sorting block time: 00:00:02 Returning block of 3468741 for bucket 145 bucket 165: 30% bucket 159: 50% Getting block 171 of 210 Reserving size (4338519) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 195: 90% Sorting block time: 00:00:02 Returning block of 2771852 for bucket 147 bucket 158: 60% bucket 202: 70% bucket 206: 70% bucket 196: 90% bucket 160: 40% bucket 208: 60% bucket 210: 60% Getting block 172 of 210 Reserving size (4338519) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: bucket 199: 80% bucket 151: 70% bucket 150: 90% bucket 198: 90% bucket 194: 100% Sorting block of length 4280616 for bucket 194 (Using difference cover) bucket 203: 80% bucket 169: 10% bucket 161: 40% bucket 155: 60% bucket 213: 70% bucket 164: 30% bucket 200: 80% bucket 153: 60% bucket 204: 70% Sorting block time: 00:00:02 Returning block of 2805699 for bucket 141 bucket 162: 40% bucket 149: 70% bucket 207: 70% Sorting block time: 00:00:03 Returning block of 4245456 for bucket 146 bucket 205: 80% Getting block 173 of 210 Reserving size (4338519) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 166: 30% bucket 197: 90% bucket 148: 80% Getting block 174 of 210 Reserving size (4338519) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 209: 70% bucket 157: 50% bucket 152: 70% bucket 212: 50% bucket 211: 60% bucket 202: 80% Sorting block time: 00:00:03 Returning block of 3048802 for bucket 191 bucket 170: 10% bucket 171: 10% bucket 201: 80% bucket 156: 60% bucket 199: 90% bucket 203: 90% bucket 195: 100% Sorting block of length 2055609 for bucket 195 (Using difference cover) bucket 210: 70% bucket 208: 70% bucket 196: 100% Sorting block of length 4201273 for bucket 196 (Using difference cover) bucket 206: 80% bucket 200: 90% bucket 213: 80% bucket 163: 40% bucket 154: 70% bucket 198: 100% Sorting block of length 3607403 for bucket 198 (Using difference cover) bucket 205: 90% bucket 168: 30% bucket 167: 40% bucket 207: 80% bucket 165: 40% bucket 204: 80% Sorting block time: 00:00:04 Returning block of 3904063 for bucket 192 bucket 172: 10% bucket 158: 70% Sorting block time: 00:00:03 Returning block of 3374762 for bucket 193 bucket 201: 90% bucket 197: 100% Sorting block of length 3736188 for bucket 197 (Using difference cover) bucket 209: 80% bucket 199: 100% Sorting block of length 3629261 for bucket 199 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2055610 for bucket 195 bucket 164: 40% bucket 169: 20% bucket 212: 60% bucket 211: 70% bucket 200: 100% Sorting block of length 2157707 for bucket 200 (Using difference cover) bucket 202: 90% bucket 213: 90% bucket 205: 100% Sorting block of length 4162909 for bucket 205 (Using difference cover) bucket 149: 80% bucket 150: 100% Sorting block of length 3430938 for bucket 150 (Using difference cover) bucket 159: 60% bucket 170: 20% bucket 203: 100% Sorting block of length 2770948 for bucket 203 (Using difference cover) bucket 160: 50% bucket 155: 70% bucket 152: 80% bucket 174: 10% bucket 208: 80% bucket 210: 80% bucket 162: 50% bucket 151: 80% bucket 206: 90% bucket 201: 100% Sorting block of length 3665179 for bucket 201 (Using difference cover) bucket 171: 20% bucket 173: 10% bucket 166: 40% bucket 207: 90% bucket 213: 100% Sorting block of length 2181625 for bucket 213 (Using difference cover) bucket 163: 50% bucket 161: 50% bucket 204: 90% Sorting block time: 00:00:03 Returning block of 4280617 for bucket 194 bucket 211: 80% bucket 148: 90% bucket 209: 90% bucket 210: 90% bucket 172: 20% bucket 156: 70% bucket 212: 70% bucket 206: 100% Sorting block of length 2306472 for bucket 206 (Using difference cover) bucket 202: 100% Sorting block of length 1964067 for bucket 202 (Using difference cover) bucket 165: 50% bucket 168: 40% bucket 157: 60% Sorting block time: 00:00:03 Returning block of 3607404 for bucket 198 bucket 208: 90% Sorting block time: 00:00:02 Returning block of 2157708 for bucket 200 bucket 170: 30% bucket 164: 50% bucket 151: 90% Sorting block time: 00:00:02 Returning block of 3629262 for bucket 199 Sorting block time: 00:00:03 Returning block of 4201274 for bucket 196 bucket 158: 80% bucket 149: 90% bucket 167: 50% bucket 211: 90% bucket 154: 80% bucket 153: 70% bucket 162: 60% bucket 171: 30% bucket 169: 30% Sorting block time: 00:00:03 Returning block of 3736189 for bucket 197 bucket 174: 20% Sorting block time: 00:00:02 Returning block of 2770949 for bucket 203 bucket 207: 100% Sorting block of length 4171000 for bucket 207 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2181626 for bucket 213 bucket 204: 100% Sorting block of length 2121338 for bucket 204 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3665180 for bucket 201 Sorting block time: 00:00:03 Returning block of 4162910 for bucket 205 bucket 209: 100% Sorting block of length 3036327 for bucket 209 (Using difference cover) bucket 208: 100% Sorting block of length 1812308 for bucket 208 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2306473 for bucket 206 bucket 212: 80% bucket 210: 100% Sorting block of length 2735767 for bucket 210 (Using difference cover) bucket 159: 70% Sorting block time: 00:00:03 Returning block of 3430939 for bucket 150 bucket 166: 50% bucket 211: 100% Sorting block of length 4049568 for bucket 211 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1964068 for bucket 202 Getting block 175 of 210 Reserving size (4338519) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 163: 60% bucket 165: 60% bucket 173: 20% bucket 152: 90% bucket 172: 30% bucket 168: 50% Sorting block time: 00:00:01 Returning block of 2121339 for bucket 204 bucket 212: 90% bucket 170: 40% bucket 162: 70% Sorting block time: 00:00:01 Returning block of 1812309 for bucket 208 bucket 164: 60% bucket 160: 60% bucket 158: 90% bucket 155: 80% bucket 169: 40% bucket 174: 30% bucket 161: 60% bucket 171: 40% Sorting block time: 00:00:02 Returning block of 2735768 for bucket 210 bucket 156: 80% Sorting block time: 00:00:02 Returning block of 3036328 for bucket 209 bucket 149: 100% Sorting block of length 4301865 for bucket 149 (Using difference cover) bucket 212: 100% Sorting block of length 2607454 for bucket 212 (Using difference cover) bucket 166: 60% Sorting block time: 00:00:02 Returning block of 4171001 for bucket 207 bucket 175: 10% bucket 163: 70% bucket 151: 100% Sorting block of length 3914460 for bucket 151 (Using difference cover) bucket 154: 90% bucket 165: 70% bucket 172: 40% bucket 153: 80% bucket 168: 60% bucket 167: 60% bucket 148: 100% Sorting block of length 4016203 for bucket 148 (Using difference cover) bucket 157: 70% bucket 159: 80% bucket 170: 50% bucket 162: 80% bucket 164: 70% bucket 173: 30% bucket 158: 100% Sorting block of length 3664449 for bucket 158 (Using difference cover) bucket 169: 50% bucket 174: 40% bucket 171: 50% Sorting block time: 00:00:03 Returning block of 4049569 for bucket 211 Sorting block time: 00:00:01 Returning block of 2607455 for bucket 212 bucket 152: 100% Sorting block of length 2777248 for bucket 152 (Using difference cover) bucket 166: 70% bucket 175: 20% bucket 163: 80% bucket 155: 90% bucket 160: 70% Sorting block time: 00:00:02 Returning block of 4301866 for bucket 149 bucket 165: 80% Sorting block time: 00:00:02 Returning block of 3914461 for bucket 151 Getting block 176 of 210 Reserving size (4338519) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: Getting block 177 of 210 Reserving size (4338519) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 161: 70% bucket 156: 90% bucket 172: 50% Sorting block time: 00:00:01 Returning block of 4016204 for bucket 148 Sorting block time: 00:00:01 Returning block of 3664450 for bucket 158 Getting block 178 of 210 Reserving size (4338519) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: Sorting block time: 00:00:02 Returning block of 2777249 for bucket 152 bucket 168: 70% bucket 170: 60% Getting block 179 of 210 Reserving size (4338519) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: Getting block 180 of 210 Reserving size (4338519) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 162: 90% bucket 164: 80% bucket 154: 100% Sorting block of length 887451 for bucket 154 (Using difference cover) bucket 173: 40% bucket 169: 60% bucket 174: 50% bucket 171: 60% Sorting block time: 00:00:00 Returning block of 887452 for bucket 154 Getting block 181 of 210 Reserving size (4338519) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 153: 90% bucket 167: 70% bucket 166: 80% bucket 175: 30% bucket 163: 90% bucket 159: 90% bucket 165: 90% bucket 177: 10% bucket 157: 80% bucket 172: 60% Exited Ebwt loop fchr[A]: 0 fchr[C]: 323920226 fchr[G]: 432422725 fchr[T]: 432422725 fchr[$]: 647885551 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 220173300 bytes to primary EBWT file: BS_GA.1.bt2 Wrote 161971392 bytes to secondary EBWT file: BS_GA.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 647885551 bwtLen: 647885552 sz: 161971388 bwtSz: 161971388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 40492847 offsSz: 161971388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3374404 numLines: 3374404 ebwtTotLen: 215961856 ebwtTotSz: 215961856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:03:25 Reading reference sizes bucket 162: 100% Sorting block of length 2649164 for bucket 162 (Using difference cover) bucket 170: 70% bucket 179: 10% bucket 164: 90% bucket 173: 50% bucket 169: 70% bucket 174: 60% bucket 171: 70% bucket 155: 100% Sorting block of length 3791328 for bucket 155 (Using difference cover) bucket 160: 80% bucket 166: 90% bucket 161: 80% bucket 176: 10% bucket 156: 100% Sorting block of length 2624800 for bucket 156 (Using difference cover) bucket 168: 80% bucket 180: 10% bucket 175: 40% bucket 178: 10% bucket 163: 100% Sorting block of length 4180454 for bucket 163 (Using difference cover) bucket 165: 100% Sorting block of length 3042490 for bucket 165 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2649165 for bucket 162 Getting block 182 of 210 Reserving size (4338519) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 177: 20% bucket 172: 70% bucket 170: 80% bucket 179: 20% bucket 153: 100% Sorting block of length 3979129 for bucket 153 (Using difference cover) bucket 167: 80% bucket 181: 10% bucket 164: 100% Sorting block of length 1793997 for bucket 164 (Using difference cover) bucket 159: 100% Sorting block of length 2208985 for bucket 159 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2624801 for bucket 156 bucket 169: 80% bucket 173: 60% bucket 174: 70% Getting block 183 of 210 Reserving size (4338519) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 171: 80% bucket 157: 90% bucket 166: 100% Sorting block of length 2078977 for bucket 166 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3042491 for bucket 165 Sorting block time: 00:00:01 Returning block of 3791329 for bucket 155 Getting block 184 of 210 Reserving size (4338519) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: Sorting block time: 00:00:00 Returning block of 1793998 for bucket 164 Getting block 185 of 210 Reserving size (4338519) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 175: 50% Getting block 186 of 210 Reserving size (4338519) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: Sorting block time: 00:00:02 Returning block of 4180455 for bucket 163 Sorting block time: 00:00:01 Returning block of 2208986 for bucket 159 Getting block 187 of 210 Reserving size (4338519) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: Getting block 188 of 210 Reserving size (4338519) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 177: 30% bucket 182: 10% Sorting block time: 00:00:01 Returning block of 2078978 for bucket 166 Getting block 189 of 210 Reserving size (4338519) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 172: 80% bucket 170: 90% bucket 160: 90% bucket 161: 90% Sorting block time: 00:00:01 Returning block of 3979130 for bucket 153 bucket 179: 30% bucket 168: 90% Getting block 190 of 210 Reserving size (4338519) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 176: 20% bucket 180: 20% bucket 178: 20% bucket 169: 90% bucket 174: 80% bucket 171: 90% bucket 173: 70% bucket 184: 10% bucket 186: 10% bucket 181: 20% bucket 167: 90% bucket 175: 60% bucket 187: 10% bucket 183: 10% bucket 177: 40% Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences bucket 189: 10% bucket 182: 20% bucket 172: 90% bucket 170: 100% Sorting block of length 1733583 for bucket 170 (Using difference cover) bucket 168: 100% Sorting block of length 1773690 for bucket 168 (Using difference cover) bucket 157: 100% Sorting block of length 4256953 for bucket 157 (Using difference cover) bucket 185: 10% bucket 171: 100% Sorting block of length 3443731 for bucket 171 (Using difference cover) bucket 169: 100% Sorting block of length 2942597 for bucket 169 (Using difference cover) bucket 174: 90% bucket 188: 10% bucket 173: 80% Sorting block time: 00:00:01 Returning block of 1733584 for bucket 170 Getting block 191 of 210 Reserving size (4338519) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 184: 20% bucket 186: 20% Sorting block time: 00:00:01 Returning block of 1773691 for bucket 168 Getting block 192 of 210 Reserving size (4338519) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 175: 70% bucket 187: 20% bucket 161: 100% Sorting block of length 2893286 for bucket 161 (Using difference cover) bucket 177: 50% Sorting block time: 00:00:01 Returning block of 2942598 for bucket 169 bucket 189: 20% bucket 160: 100% Sorting block of length 2663209 for bucket 160 (Using difference cover) Getting block 193 of 210 Reserving size (4338519) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 190: 10% bucket 172: 100% Sorting block of length 3025217 for bucket 172 (Using difference cover) bucket 182: 30% bucket 176: 30% bucket 179: 40% Sorting block time: 00:00:02 Returning block of 4256954 for bucket 157 bucket 180: 30% Sorting block time: 00:00:01 Returning block of 3443732 for bucket 171 Getting block 194 of 210 Reserving size (4338519) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 178: 30% Getting block 195 of 210 Reserving size (4338519) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 174: 100% Sorting block of length 4124921 for bucket 174 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2893287 for bucket 161 Getting block 196 of 210 Reserving size (4338519) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 173: 90% Sorting block time: 00:00:01 Returning block of 2663210 for bucket 160 Getting block 197 of 210 Reserving size (4338519) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 191: 10% bucket 181: 30% Sorting block time: 00:00:02 Returning block of 3025218 for bucket 172 bucket 184: 30% bucket 192: 10% bucket 186: 30% Getting block 198 of 210 Reserving size (4338519) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 167: 100% Sorting block of length 3002730 for bucket 167 (Using difference cover) bucket 187: 30% bucket 175: 80% bucket 177: 60% bucket 183: 20% bucket 189: 30% bucket 193: 10% bucket 182: 40% bucket 195: 10% bucket 185: 20% bucket 188: 20% Sorting block time: 00:00:02 Returning block of 4124922 for bucket 174 Getting block 199 of 210 Reserving size (4338519) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: Sorting block time: 00:00:01 Returning block of 3002731 for bucket 167 bucket 173: 100% Sorting block of length 3596434 for bucket 173 (Using difference cover) Getting block 200 of 210 Reserving size (4338519) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 191: 20% bucket 184: 40% bucket 186: 40% bucket 198: 10% bucket 187: 40% bucket 175: 90% bucket 190: 20% bucket 192: 20% bucket 179: 50% bucket 176: 40% bucket 180: 40% bucket 194: 10% bucket 177: 70% bucket 178: 40% bucket 189: 40% bucket 196: 10% bucket 193: 20% bucket 197: 10% bucket 181: 40% bucket 182: 50% bucket 195: 20% bucket 199: 10% Sorting block time: 00:00:02 Returning block of 3596435 for bucket 173 bucket 183: 30% Getting block 201 of 210 Reserving size (4338519) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Time to join reference sequences: 00:00:07 Time to reverse reference sequence: 00:00:00 bmax according to bmaxDivN setting: 5784692 Using parameters --bmax 4338519 --dcv 1024 Doing ahead-of-time memory usage test bucket 191: 30% bucket 186: 50% bucket 198: 20% bucket 184: 50% bucket 175: 100% Sorting block of length 2265237 for bucket 175 (Using difference cover) bucket 187: 50% bucket 192: 30% bucket 185: 30% bucket 188: 30% bucket 177: 80% bucket 189: 50% bucket 193: 30% bucket 194: 20% bucket 200: 10% Passed! Constructing with these parameters: --bmax 4338519 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime bucket 182: 60% bucket 195: 30% Building sPrimeOrder V-Sorting samples Sorting block time: 00:00:01 Returning block of 2265238 for bucket 175 bucket 199: 20% Getting block 202 of 210 Reserving size (4338519) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 190: 30% bucket 176: 50% bucket 179: 60% bucket 180: 50% bucket 191: 40% bucket 186: 60% bucket 198: 30% bucket 184: 60% bucket 187: 60% bucket 192: 40% bucket 178: 50% bucket 201: 10% bucket 196: 20% bucket 197: 20% bucket 177: 90% bucket 189: 60% bucket 181: 50% bucket 193: 40% bucket 194: 30% bucket 183: 40% bucket 195: 40% bucket 182: 70% bucket 199: 30% bucket 185: 40% bucket 188: 40% bucket 186: 70% bucket 198: 40% bucket 191: 50% bucket 187: 70% bucket 184: 70% bucket 192: 50% bucket 201: 20% bucket 200: 20% bucket 177: 100% Sorting block of length 2610876 for bucket 177 (Using difference cover) bucket 189: 70% bucket 194: 40% bucket 193: 50% bucket 202: 10% bucket 190: 40% bucket 180: 60% bucket 179: 70% bucket 195: 50% bucket 176: 60% bucket 182: 80% bucket 199: 40% Sorting block time: 00:00:01 Returning block of 2610877 for bucket 177 Getting block 203 of 210 Reserving size (4338519) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 178: 60% bucket 196: 30% bucket 197: 30% bucket 181: 60% bucket 191: 60% bucket 184: 80% bucket 186: 80% bucket 198: 50% bucket 183: 50% bucket 201: 30% bucket 187: 80% bucket 185: 50% bucket 192: 60% bucket 195: 60% bucket 189: 80% V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output bucket 203: 10% bucket 194: 50% bucket 193: 60% bucket 199: 50% bucket 182: 90% bucket 184: 90% bucket 188: 50% bucket 202: 20% bucket 198: 60% bucket 190: 50% bucket 200: 30% bucket 191: 70% bucket 186: 90% bucket 201: 40% bucket 180: 70% bucket 181: 70% bucket 187: 90% bucket 195: 70% bucket 192: 70% bucket 196: 40% bucket 179: 80% bucket 189: 90% bucket 176: 70% bucket 178: 70% bucket 203: 20% bucket 197: 40% bucket 194: 60% bucket 193: 70% bucket 199: 60% bucket 182: 100% Sorting block of length 3991909 for bucket 182 (Using difference cover) bucket 185: 60% bucket 184: 100% Sorting block of length 3696813 for bucket 184 (Using difference cover) bucket 183: 60% bucket 198: 70% bucket 186: 100% Sorting block of length 3678224 for bucket 186 (Using difference cover) bucket 191: 80% bucket 201: 50% bucket 187: 100% Sorting block of length 4138835 for bucket 187 (Using difference cover) Ranking v-sort output time: 00:00:04 Invoking Larsson-Sadakane on ranks bucket 192: 80% bucket 195: 80% bucket 189: 100% Sorting block of length 4278620 for bucket 189 (Using difference cover) bucket 203: 30% bucket 194: 70% bucket 199: 70% bucket 193: 80% bucket 188: 60% Sorting block time: 00:00:02 Returning block of 3696814 for bucket 184 Sorting block time: 00:00:02 Returning block of 3991910 for bucket 182 Getting block 204 of 210 Reserving size (4338519) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: Getting block 205 of 210 Reserving size (4338519) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:01 Returning block of 3678225 for bucket 186 Getting block 206 of 210 Reserving size (4338519) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 190: 60% bucket 202: 30% bucket 198: 80% bucket 200: 40% bucket 201: 60% bucket 191: 90% bucket 180: 80% bucket 181: 80% Sorting block time: 00:00:02 Returning block of 4138836 for bucket 187 Getting block 207 of 210 Reserving size (4338519) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 196: 50% bucket 192: 90% bucket 195: 90% Sorting block time: 00:00:02 Returning block of 4278621 for bucket 189 bucket 185: 70% bucket 179: 90% Getting block 208 of 210 Reserving size (4338519) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 203: 40% bucket 176: 80% bucket 178: 80% bucket 197: 50% bucket 194: 80% bucket 199: 80% bucket 183: 70% bucket 193: 90% bucket 205: 10% bucket 206: 10% bucket 198: 90% bucket 201: 70% bucket 191: 100% Sorting block of length 3571824 for bucket 191 (Using difference cover) bucket 207: 10% bucket 192: 100% Sorting block of length 3248486 for bucket 192 (Using difference cover) bucket 195: 100% Sorting block of length 3251093 for bucket 195 (Using difference cover) bucket 208: 10% bucket 185: 80% bucket 203: 50% bucket 204: 10% bucket 194: 90% bucket 199: 90% bucket 205: 20% bucket 188: 70% bucket 193: 100% Sorting block of length 3968449 for bucket 193 (Using difference cover) bucket 190: 70% bucket 202: 40% bucket 206: 20% bucket 200: 50% Sorting block time: 00:00:02 Returning block of 3571825 for bucket 191 bucket 180: 90% bucket 198: 100% Sorting block of length 1571762 for bucket 198 (Using difference cover) Invoking Larsson-Sadakane on ranks time: 00:00:06 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes bucket 181: 90% Getting block 209 of 210 Reserving size (4338519) for bucket 209 Calculating Z arrays for bucket 209 Entering block accumulator loop for bucket 209: bucket 201: 80% bucket 179: 100% Sorting block of length 4314054 for bucket 179 (Using difference cover) bucket 196: 60% Sorting block time: 00:00:02 Returning block of 3251094 for bucket 195 bucket 176: 90% Getting block 210 of 210 Reserving size (4338519) for bucket 210 Calculating Z arrays for bucket 210 Entering block accumulator loop for bucket 210: Sorting block time: 00:00:02 Returning block of 3248487 for bucket 192 bucket 207: 20% bucket 183: 80% bucket 178: 90% bucket 197: 60% bucket 203: 60% bucket 208: 20% bucket 185: 90% bucket 210: 10% bucket 194: 100% Sorting block of length 2944758 for bucket 194 (Using difference cover) Sorting block time: 00:00:02 Returning block of 1571763 for bucket 198 bucket 205: 30% bucket 199: 100% Sorting block of length 4332930 for bucket 199 (Using difference cover) bucket 204: 20% bucket 210: 20% bucket 181: 100% Sorting block of length 4048686 for bucket 181 (Using difference cover) bucket 206: 30% bucket 188: 80% bucket 190: 80% bucket 209: 10% bucket 180: 100% Sorting block of length 797673 for bucket 180 (Using difference cover) bucket 201: 90% bucket 183: 90% bucket 197: 70% bucket 200: 60% bucket 202: 50% bucket 178: 100% Sorting block of length 3084593 for bucket 178 (Using difference cover) bucket 207: 30% Sorting block time: 00:00:04 Returning block of 3968450 for bucket 193 bucket 176: 100% Sorting block of length 4100407 for bucket 176 (Using difference cover) bucket 196: 70% bucket 208: 30% Sorting block time: 00:00:03 Returning block of 4314055 for bucket 179 Sorting block time: 00:00:00 Returning block of 797674 for bucket 180 bucket 203: 70% bucket 185: 100% Sorting block of length 4117246 for bucket 185 (Using difference cover) bucket 206: 40% bucket 210: 30% bucket 205: 40% Sorting block time: 00:00:03 Returning block of 2944759 for bucket 194 bucket 200: 70% bucket 188: 90% bucket 197: 80% bucket 190: 90% bucket 209: 20% bucket 204: 30% Sorting block time: 00:00:03 Returning block of 4048687 for bucket 181 Sorting block time: 00:00:02 Returning block of 3084594 for bucket 178 bucket 201: 100% Sorting block of length 935553 for bucket 201 (Using difference cover) Splitting and merging Splitting and merging time: 00:00:00 Split 41, merged 122; iterating... bucket 207: 40% Sorting block time: 00:00:02 Returning block of 4100408 for bucket 176 bucket 202: 60% bucket 208: 40% Sorting block time: 00:00:03 Returning block of 4332931 for bucket 199 bucket 183: 100% Sorting block of length 1990736 for bucket 183 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4117247 for bucket 185 Sorting block time: 00:00:01 Returning block of 935554 for bucket 201 bucket 210: 40% bucket 206: 50% bucket 203: 80% bucket 196: 80% bucket 205: 50% Sorting block time: 00:00:01 Returning block of 1990737 for bucket 183 bucket 190: 100% Sorting block of length 3740308 for bucket 190 (Using difference cover) bucket 207: 50% bucket 188: 100% Sorting block of length 3520547 for bucket 188 (Using difference cover) bucket 210: 50% bucket 209: 30% bucket 208: 50% bucket 204: 40% bucket 197: 90% bucket 200: 80% bucket 202: 70% bucket 206: 60% bucket 207: 60% Sorting block time: 00:00:02 Returning block of 3740309 for bucket 190 Splitting and merging Splitting and merging time: 00:00:00 Split 19, merged 23; iterating... bucket 196: 90% bucket 203: 90% bucket 210: 60% bucket 205: 60% bucket 204: 50% bucket 200: 90% Sorting block time: 00:00:03 Returning block of 3520548 for bucket 188 bucket 208: 60% bucket 206: 70% bucket 197: 100% Sorting block of length 2865380 for bucket 197 (Using difference cover) bucket 202: 80% bucket 210: 70% bucket 209: 40% bucket 196: 100% Sorting block of length 3979501 for bucket 196 (Using difference cover) bucket 207: 70% bucket 203: 100% Sorting block of length 630598 for bucket 203 (Using difference cover) bucket 210: 80% Sorting block time: 00:00:00 Returning block of 630599 for bucket 203 bucket 205: 70% bucket 200: 100% Sorting block of length 3594192 for bucket 200 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2865381 for bucket 197 bucket 204: 60% bucket 202: 90% Sorting block time: 00:00:02 Returning block of 3979502 for bucket 196 bucket 208: 70% bucket 209: 50% bucket 210: 90% bucket 206: 80% bucket 207: 80% Splitting and merging Splitting and merging time: 00:00:00 Split 9, merged 16; iterating... Sorting block time: 00:00:02 Returning block of 3594193 for bucket 200 bucket 205: 80% bucket 204: 70% bucket 210: 100% Sorting block of length 2498156 for bucket 210 (Using difference cover) bucket 202: 100% Sorting block of length 3885715 for bucket 202 (Using difference cover) bucket 209: 60% bucket 208: 80% bucket 207: 90% bucket 205: 90% Sorting block time: 00:00:01 Returning block of 2498157 for bucket 210 bucket 206: 90% bucket 204: 80% Sorting block time: 00:00:02 Returning block of 3885716 for bucket 202 Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 6; iterating... bucket 209: 70% bucket 207: 100% Sorting block of length 3751634 for bucket 207 (Using difference cover) bucket 208: 90% bucket 206: 100% Sorting block of length 3524738 for bucket 206 (Using difference cover) bucket 205: 100% Sorting block of length 2159646 for bucket 205 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2159647 for bucket 205 bucket 208: 100% Sorting block of length 2836101 for bucket 208 (Using difference cover) bucket 209: 80% bucket 204: 90% Sorting block time: 00:00:02 Returning block of 3751635 for bucket 207 Sorting block time: 00:00:03 Returning block of 3524739 for bucket 206 Sorting block time: 00:00:02 Returning block of 2836102 for bucket 208 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 2; iterating... Avg bucket size: 3.14507e+06 (target: 4338518) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 206 Reserving size (4338519) for bucket 1 Getting block 2 of 206 Getting block 3 of 206 Getting block 4 of 206 Getting block 5 of 206 Getting block 6 of 206 Getting block 7 of 206 Getting block 8 of 206 Getting block 9 of 206 Getting block 10 of 206 Getting block 11 of 206 Getting block 12 of 206 Getting block 13 of 206 Getting block 14 of 206 Getting block 15 of 206 Getting block 16 of 206 Getting block 17 of 206 Calculating Z arrays for bucket 1 Reserving size (4338519) for bucket 2 Reserving size (4338519) for bucket 3 Reserving size (4338519) for bucket 4 Getting block 18 of 206 Getting block 19 of 206 Getting block 20 of 206 Getting block 21 of 206 Getting block 22 of 206 Getting block 23 of 206 Getting block 24 of 206 Getting block 25 of 206 Getting block 26 of 206 Reserving size (4338519) for bucket 5 Reserving size (4338519) for bucket 6 Reserving size (4338519) for bucket 7 Reserving size (4338519) for bucket 8 Reserving size (4338519) for bucket 9 Reserving size (4338519) for bucket 10 Reserving size (4338519) for bucket 11 Reserving size (4338519) for bucket 12 Reserving size (4338519) for bucket 13 Reserving size (4338519) for bucket 14 Reserving size (4338519) for bucket 15 Reserving size (4338519) for bucket 16 Reserving size (4338519) for bucket 17 Getting block 27 of 206 Entering block accumulator loop for bucket 1: Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Reserving size (4338519) for bucket 18 Reserving size (4338519) for bucket 19 Reserving size (4338519) for bucket 20 Reserving size (4338519) for bucket 21 Reserving size (4338519) for bucket 22 Reserving size (4338519) for bucket 23 Reserving size (4338519) for bucket 24 Reserving size (4338519) for bucket 25 Reserving size (4338519) for bucket 26 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 17 Reserving size (4338519) for bucket 27 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Calculating Z arrays for bucket 18 Entering block accumulator loop for bucket 4: Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 13: Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: Entering block accumulator loop for bucket 27: bucket 209: 90% bucket 204: 100% Sorting block of length 3909600 for bucket 204 (Using difference cover) bucket 1: 10% bucket 3: 10% bucket 2: 10% bucket 8: 10% bucket 14: 10% bucket 9: 10% bucket 11: 10% bucket 4: 10% bucket 5: 10% bucket 7: 10% bucket 15: 10% bucket 12: 10% bucket 19: 10% bucket 6: 10% bucket 13: 10% bucket 10: 10% bucket 22: 10% bucket 20: 10% bucket 26: 10% bucket 16: 10% bucket 18: 10% bucket 25: 10% bucket 23: 10% bucket 17: 10% bucket 21: 10% bucket 24: 10% bucket 27: 10% bucket 1: 20% bucket 2: 20% bucket 3: 20% bucket 8: 20% bucket 14: 20% bucket 4: 20% bucket 11: 20% bucket 5: 20% bucket 7: 20% bucket 15: 20% bucket 12: 20% bucket 19: 20% bucket 209: 100% Sorting block of length 3916414 for bucket 209 (Using difference cover) bucket 13: 20% bucket 9: 20% bucket 22: 20% bucket 20: 20% bucket 16: 20% bucket 18: 20% bucket 26: 20% bucket 25: 20% bucket 17: 20% bucket 23: 20% bucket 6: 20% bucket 10: 20% bucket 21: 20% bucket 3: 30% bucket 1: 30% bucket 2: 30% bucket 27: 20% bucket 8: 30% bucket 4: 30% bucket 24: 20% bucket 11: 30% bucket 14: 30% bucket 5: 30% bucket 7: 30% bucket 15: 30% bucket 12: 30% bucket 19: 30% bucket 9: 30% bucket 22: 30% bucket 20: 30% bucket 16: 30% bucket 17: 30% bucket 26: 30% bucket 25: 30% bucket 23: 30% bucket 10: 30% bucket 13: 30% bucket 6: 30% bucket 18: 30% bucket 1: 40% bucket 2: 40% bucket 3: 40% bucket 21: 30% Sorting block time: 00:00:03 Returning block of 3909601 for bucket 204 bucket 8: 40% bucket 4: 40% bucket 11: 40% bucket 5: 40% bucket 14: 40% bucket 7: 40% bucket 27: 30% bucket 15: 40% bucket 12: 40% bucket 19: 40% bucket 9: 40% bucket 17: 40% bucket 22: 40% bucket 20: 40% bucket 24: 30% bucket 26: 40% bucket 10: 40% bucket 23: 40% bucket 25: 40% bucket 6: 40% bucket 16: 40% bucket 18: 40% bucket 13: 40% bucket 1: 50% bucket 3: 50% bucket 2: 50% bucket 8: 50% bucket 4: 50% bucket 21: 40% bucket 11: 50% bucket 5: 50% bucket 7: 50% bucket 14: 50% bucket 15: 50% bucket 27: 40% bucket 12: 50% bucket 19: 50% bucket 9: 50% Sorting block time: 00:00:03 Returning block of 3916415 for bucket 209 bucket 17: 50% bucket 22: 50% bucket 20: 50% bucket 10: 50% bucket 26: 50% bucket 25: 50% bucket 6: 50% bucket 16: 50% bucket 1: 60% bucket 24: 40% bucket 2: 60% bucket 3: 60% bucket 13: 50% bucket 18: 50% bucket 23: 50% bucket 8: 60% bucket 4: 60% bucket 11: 60% bucket 5: 60% bucket 21: 50% bucket 7: 60% bucket 14: 60% bucket 15: 60% bucket 12: 60% bucket 19: 60% bucket 27: 50% bucket 9: 60% bucket 17: 60% bucket 10: 60% bucket 22: 60% bucket 20: 60% bucket 1: 70% bucket 2: 70% bucket 3: 70% bucket 6: 60% bucket 26: 60% bucket 25: 60% bucket 16: 60% bucket 13: 60% bucket 18: 60% bucket 24: 50% bucket 23: 60% bucket 8: 70% bucket 4: 70% bucket 11: 70% bucket 5: 70% bucket 7: 70% bucket 21: 60% bucket 14: 70% bucket 15: 70% bucket 12: 70% bucket 19: 70% bucket 17: 70% bucket 9: 70% bucket 27: 60% bucket 10: 70% bucket 1: 80% bucket 3: 80% bucket 2: 80% bucket 22: 70% bucket 20: 70% bucket 6: 70% bucket 26: 70% bucket 25: 70% bucket 13: 70% bucket 16: 70% bucket 18: 70% bucket 24: 60% bucket 8: 80% bucket 23: 70% bucket 4: 80% bucket 5: 80% bucket 11: 80% bucket 7: 80% bucket 14: 80% bucket 21: 70% bucket 15: 80% bucket 12: 80% bucket 19: 80% bucket 17: 80% bucket 9: 80% bucket 1: 90% bucket 10: 80% bucket 2: 90% bucket 3: 90% bucket 27: 70% bucket 6: 80% bucket 22: 80% bucket 20: 80% bucket 13: 80% bucket 16: 80% bucket 25: 80% bucket 26: 80% bucket 18: 80% bucket 8: 90% bucket 4: 90% bucket 23: 80% bucket 24: 70% bucket 5: 90% bucket 11: 90% bucket 7: 90% bucket 14: 90% bucket 21: 80% bucket 15: 90% bucket 1: 100% Sorting block of length 3065168 for bucket 1 (Using difference cover) bucket 12: 90% bucket 19: 90% bucket 17: 90% bucket 9: 90% bucket 2: 100% bucket 3: 100% Sorting block of length 3484204 for bucket 2 Sorting block of length 2998326 for bucket 3 (Using difference cover) (Using difference cover) bucket 10: 90% bucket 27: 80% bucket 6: 90% bucket 22: 90% bucket 20: 90% bucket 13: 90% bucket 8: 100% Sorting block of length 3302650 for bucket 8 (Using difference cover) bucket 4: 100% Sorting block of length 4085347 for bucket 4 (Using difference cover) bucket 16: 90% bucket 18: 90% bucket 25: 90% bucket 26: 90% bucket 23: 90% bucket 5: 100% Sorting block of length 4196574 for bucket 5 (Using difference cover) bucket 11: 100% Sorting block of length 2640243 for bucket 11 (Using difference cover) bucket 7: 100% Sorting block of length 3011032 for bucket 7 (Using difference cover) bucket 24: 80% bucket 14: 100% Sorting block of length 3454410 for bucket 14 (Using difference cover) bucket 21: 90% bucket 15: 100% Sorting block of length 3367836 for bucket 15 (Using difference cover) bucket 17: 100% Sorting block of length 1123710 for bucket 17 (Using difference cover) bucket 9: 100% Sorting block of length 3605867 for bucket 9 (Using difference cover) bucket 19: 100% Sorting block of length 1786108 for bucket 19 (Using difference cover) bucket 12: 100% Sorting block of length 2097504 for bucket 12 (Using difference cover) bucket 10: 100% Sorting block of length 2467988 for bucket 10 (Using difference cover) bucket 6: 100% Sorting block of length 4203610 for bucket 6 (Using difference cover) bucket 13: 100% Sorting block of length 3227453 for bucket 13 (Using difference cover) bucket 22: 100% Sorting block of length 4150878 for bucket 22 (Using difference cover) bucket 20: 100% Sorting block of length 3558784 for bucket 20 (Using difference cover) bucket 18: 100% Sorting block of length 3278694 for bucket 18 (Using difference cover) bucket 27: 90% bucket 16: 100% Sorting block of length 3819051 for bucket 16 (Using difference cover) bucket 25: 100% Sorting block of length 3729625 for bucket 25 (Using difference cover) bucket 23: 100% Sorting block of length 1203857 for bucket 23 (Using difference cover) bucket 26: 100% Sorting block of length 2617589 for bucket 26 (Using difference cover) bucket 24: 90% Sorting block time: 00:00:01 Returning block of 1123711 for bucket 17 Sorting block time: 00:00:02 Returning block of 3065169 for bucket 1 Getting block 28 of 206 Reserving size (4338519) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: Getting block 29 of 206 Reserving size (4338519) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 21: 100% Sorting block of length 4086653 for bucket 21 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2998327 for bucket 3 Getting block 30 of 206 Reserving size (4338519) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:02 Returning block of 3484205 for bucket 2 Sorting block time: 00:00:01 Returning block of 1786109 for bucket 19 Sorting block time: 00:00:01 Returning block of 2640244 for bucket 11 Getting block 31 of 206 Reserving size (4338519) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: Getting block 32 of 206 Reserving size (4338519) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: Getting block 33 of 206 Reserving size (4338519) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Sorting block time: 00:00:00 Returning block of 1203858 for bucket 23 bucket 27: 100% Sorting block of length 3718867 for bucket 27 (Using difference cover) Getting block 34 of 206 Reserving size (4338519) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: Sorting block time: 00:00:01 Returning block of 2097505 for bucket 12 Getting block 35 of 206 Reserving size (4338519) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:01 Returning block of 3302651 for bucket 8 Sorting block time: 00:00:01 Returning block of 3011033 for bucket 7 Sorting block time: 00:00:01 Returning block of 2467989 for bucket 10 bucket 24: 100% Sorting block of length 4304587 for bucket 24 (Using difference cover) Getting block 36 of 206 Reserving size (4338519) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Getting block 37 of 206 Reserving size (4338519) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Getting block 38 of 206 Reserving size (4338519) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: bucket 28: 10% bucket 29: 10% Sorting block time: 00:00:02 Returning block of 3454411 for bucket 14 Sorting block time: 00:00:02 Returning block of 4085348 for bucket 4 Sorting block time: 00:00:02 Returning block of 3367837 for bucket 15 bucket 30: 10% Getting block 39 of 206 Reserving size (4338519) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: Getting block 40 of 206 Reserving size (4338519) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Getting block 41 of 206 Reserving size (4338519) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:02 Returning block of 3605868 for bucket 9 Sorting block time: 00:00:02 Returning block of 4196575 for bucket 5 bucket 31: 10% Sorting block time: 00:00:01 Returning block of 2617590 for bucket 26 bucket 33: 10% Sorting block time: 00:00:02 Returning block of 3227454 for bucket 13 Getting block 42 of 206 Reserving size (4338519) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Getting block 43 of 206 Reserving size (4338519) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Getting block 44 of 206 Reserving size (4338519) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Sorting block time: 00:00:01 Returning block of 3278695 for bucket 18 bucket 34: 10% bucket 32: 10% Getting block 45 of 206 Reserving size (4338519) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Sorting block time: 00:00:02 Returning block of 3558785 for bucket 20 Getting block 46 of 206 Reserving size (4338519) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: bucket 35: 10% Getting block 47 of 206 Reserving size (4338519) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 36: 10% Sorting block time: 00:00:02 Returning block of 4203611 for bucket 6 bucket 28: 20% Sorting block time: 00:00:01 Returning block of 3729626 for bucket 25 Sorting block time: 00:00:01 Returning block of 3819052 for bucket 16 bucket 29: 20% bucket 37: 10% bucket 38: 10% Sorting block time: 00:00:02 Returning block of 4150879 for bucket 22 Getting block 48 of 206 Reserving size (4338519) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Getting block 49 of 206 Reserving size (4338519) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Getting block 50 of 206 Reserving size (4338519) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: Getting block 51 of 206 Reserving size (4338519) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 30: 20% bucket 39: 10% bucket 41: 10% bucket 31: 20% bucket 40: 10% Sorting block time: 00:00:02 Returning block of 4086654 for bucket 21 bucket 33: 20% bucket 42: 10% bucket 34: 20% bucket 43: 10% Getting block 52 of 206 Reserving size (4338519) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: bucket 44: 10% bucket 45: 10% bucket 32: 20% bucket 46: 10% Sorting block time: 00:00:02 Returning block of 3718868 for bucket 27 bucket 35: 20% bucket 36: 20% Getting block 53 of 206 Reserving size (4338519) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 47: 10% bucket 28: 30% bucket 37: 20% bucket 48: 10% bucket 29: 30% bucket 38: 20% bucket 49: 10% Sorting block time: 00:00:02 Returning block of 4304588 for bucket 24 bucket 30: 30% bucket 50: 10% bucket 41: 20% bucket 51: 10% bucket 31: 30% Getting block 54 of 206 Reserving size (4338519) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 39: 20% bucket 40: 20% bucket 33: 30% bucket 42: 20% bucket 34: 30% bucket 32: 30% bucket 52: 10% bucket 44: 20% bucket 45: 20% bucket 46: 20% bucket 35: 30% bucket 43: 20% bucket 36: 30% bucket 53: 10% bucket 37: 30% bucket 29: 40% bucket 47: 20% bucket 38: 30% bucket 49: 20% bucket 48: 20% bucket 28: 40% bucket 30: 40% bucket 31: 40% bucket 41: 30% bucket 50: 20% bucket 51: 20% bucket 39: 30% bucket 40: 30% bucket 33: 40% bucket 34: 40% bucket 42: 30% bucket 54: 10% bucket 32: 40% bucket 35: 40% bucket 44: 30% bucket 52: 20% bucket 46: 30% bucket 45: 30% bucket 36: 40% bucket 43: 30% bucket 53: 20% bucket 29: 50% bucket 37: 40% bucket 38: 40% bucket 47: 30% bucket 48: 30% bucket 49: 30% bucket 31: 50% bucket 30: 50% bucket 41: 40% bucket 28: 50% bucket 39: 40% bucket 51: 30% bucket 50: 30% bucket 33: 50% bucket 34: 50% bucket 40: 40% bucket 32: 50% bucket 42: 40% bucket 54: 20% bucket 35: 50% bucket 46: 40% bucket 45: 40% bucket 36: 50% bucket 44: 40% bucket 53: 30% bucket 29: 60% bucket 52: 30% bucket 43: 40% bucket 37: 50% bucket 38: 50% bucket 47: 40% bucket 49: 40% bucket 31: 60% bucket 48: 40% bucket 30: 60% bucket 28: 60% bucket 41: 50% bucket 39: 50% bucket 33: 60% bucket 51: 40% bucket 50: 40% bucket 34: 60% bucket 32: 60% bucket 40: 50% bucket 35: 60% bucket 46: 50% bucket 54: 30% bucket 42: 50% bucket 36: 60% bucket 29: 70% bucket 44: 50% bucket 53: 40% bucket 52: 40% bucket 37: 60% bucket 45: 50% bucket 38: 60% bucket 31: 70% bucket 43: 50% bucket 47: 50% bucket 49: 50% bucket 48: 50% bucket 28: 70% bucket 39: 60% bucket 30: 70% bucket 41: 60% bucket 33: 70% bucket 51: 50% bucket 34: 70% bucket 32: 70% bucket 50: 50% bucket 40: 60% bucket 35: 70% bucket 46: 60% bucket 29: 80% bucket 42: 60% bucket 36: 70% bucket 44: 60% bucket 53: 50% bucket 37: 70% bucket 38: 70% bucket 45: 60% bucket 31: 80% bucket 52: 50% bucket 54: 40% bucket 39: 70% bucket 49: 60% bucket 47: 60% bucket 30: 80% bucket 43: 60% bucket 41: 70% bucket 48: 60% bucket 33: 80% bucket 34: 80% bucket 51: 60% bucket 32: 80% bucket 28: 80% bucket 50: 60% bucket 35: 80% bucket 40: 70% bucket 29: 90% bucket 46: 70% bucket 36: 80% bucket 42: 70% bucket 44: 70% bucket 53: 60% bucket 37: 80% bucket 31: 90% bucket 38: 80% bucket 45: 70% bucket 39: 80% bucket 54: 50% bucket 30: 90% bucket 41: 80% bucket 43: 70% bucket 49: 70% bucket 33: 90% bucket 47: 70% bucket 48: 70% bucket 52: 60% bucket 34: 90% bucket 32: 90% bucket 28: 90% bucket 51: 70% bucket 35: 90% bucket 50: 70% bucket 29: 100% Sorting block of length 3187622 for bucket 29 (Using difference cover) bucket 46: 80% bucket 36: 90% bucket 42: 80% bucket 44: 80% bucket 40: 80% bucket 31: 100% Sorting block of length 4023565 for bucket 31 (Using difference cover) bucket 37: 90% bucket 38: 90% bucket 53: 70% bucket 39: 90% bucket 30: 100% Sorting block of length 4082719 for bucket 30 (Using difference cover) bucket 45: 80% bucket 33: 100% Sorting block of length 3731607 for bucket 33 (Using difference cover) bucket 41: 90% bucket 43: 80% bucket 47: 80% bucket 34: 100% Sorting block of length 2168763 for bucket 34 (Using difference cover) bucket 48: 80% bucket 32: 100% Sorting block of length 3308870 for bucket 32 (Using difference cover) bucket 28: 100% Sorting block of length 1763123 for bucket 28 (Using difference cover) bucket 49: 80% bucket 54: 60% bucket 51: 80% bucket 52: 70% bucket 35: 100% Sorting block of length 2552947 for bucket 35 (Using difference cover) bucket 50: 80% bucket 42: 90% bucket 46: 90% bucket 36: 100% Sorting block of length 4001701 for bucket 36 (Using difference cover) bucket 44: 90% bucket 37: 100% Sorting block of length 3783136 for bucket 37 (Using difference cover) bucket 40: 90% bucket 38: 100% Sorting block of length 3273074 for bucket 38 (Using difference cover) bucket 53: 80% bucket 39: 100% Sorting block of length 1111266 for bucket 39 (Using difference cover) bucket 41: 100% Sorting block of length 3682028 for bucket 41 (Using difference cover) bucket 45: 90% bucket 43: 90% bucket 47: 90% Sorting block time: 00:00:01 Returning block of 1763124 for bucket 28 bucket 49: 90% bucket 48: 90% Getting block 55 of 206 Reserving size (4338519) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 51: 90% bucket 54: 70% Sorting block time: 00:00:01 Returning block of 3187623 for bucket 29 Sorting block time: 00:00:01 Returning block of 2168764 for bucket 34 Getting block 56 of 206 Reserving size (4338519) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: bucket 52: 80% Getting block 57 of 206 Reserving size (4338519) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: bucket 50: 90% bucket 42: 100% Sorting block of length 3643639 for bucket 42 (Using difference cover) bucket 46: 100% Sorting block of length 1362286 for bucket 46 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1111267 for bucket 39 Getting block 58 of 206 Reserving size (4338519) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:01 Returning block of 2552948 for bucket 35 bucket 40: 100% Sorting block of length 3855010 for bucket 40 (Using difference cover) Getting block 59 of 206 Reserving size (4338519) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 53: 90% Sorting block time: 00:00:02 Returning block of 4023566 for bucket 31 bucket 44: 100% Sorting block of length 2122690 for bucket 44 (Using difference cover) Getting block 60 of 206 Reserving size (4338519) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: bucket 45: 100% Sorting block of length 4190016 for bucket 45 (Using difference cover) bucket 43: 100% Sorting block of length 3703482 for bucket 43 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3308871 for bucket 32 Sorting block time: 00:00:02 Returning block of 3731608 for bucket 33 bucket 49: 100% Sorting block of length 2000945 for bucket 49 (Using difference cover) bucket 48: 100% Sorting block of length 85783 for bucket 48 (Using difference cover) bucket 47: 100% Sorting block of length 4690482 for bucket 47 (Using difference cover) Sorting block time: 00:00:00 Returning block of 85784 for bucket 48 Getting block 61 of 206 Reserving size (4338519) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: Getting block 62 of 206 Reserving size (4338519) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: Getting block 63 of 206 Reserving size (4338519) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: Sorting block time: 00:00:02 Returning block of 4082720 for bucket 30 bucket 51: 100% Sorting block of length 576093 for bucket 51 (Using difference cover) bucket 55: 10% bucket 54: 80% Sorting block time: 00:00:01 Returning block of 1362287 for bucket 46 bucket 56: 10% Getting block 64 of 206 Reserving size (4338519) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: bucket 52: 90% bucket 57: 10% Getting block 65 of 206 Reserving size (4338519) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 50: 100% Sorting block of length 4316824 for bucket 50 (Using difference cover) Sorting block time: 00:00:00 Returning block of 576094 for bucket 51 Getting block 66 of 206 Reserving size (4338519) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: Sorting block time: 00:00:01 Returning block of 3273075 for bucket 38 Getting block 67 of 206 Reserving size (4338519) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: bucket 58: 10% Sorting block time: 00:00:01 Returning block of 4001702 for bucket 36 bucket 59: 10% bucket 53: 100% Sorting block of length 1912788 for bucket 53 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3783137 for bucket 37 Getting block 68 of 206 Reserving size (4338519) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: bucket 60: 10% Sorting block time: 00:00:02 Returning block of 3682029 for bucket 41 Sorting block time: 00:00:01 Returning block of 2122691 for bucket 44 Getting block 69 of 206 Reserving size (4338519) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: Getting block 70 of 206 Reserving size (4338519) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: bucket 63: 10% bucket 62: 10% Sorting block time: 00:00:01 Returning block of 2000946 for bucket 49 Getting block 71 of 206 Reserving size (4338519) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 61: 10% Getting block 72 of 206 Reserving size (4338519) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: bucket 55: 20% bucket 54: 90% bucket 56: 20% bucket 52: 100% Sorting block of length 4034066 for bucket 52 (Using difference cover) bucket 64: 10% bucket 57: 20% bucket 65: 10% Sorting block time: 00:00:02 Returning block of 3643640 for bucket 42 Getting block 73 of 206 Reserving size (4338519) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 66: 10% Sorting block time: 00:00:02 Returning block of 3855011 for bucket 40 bucket 67: 10% Sorting block time: 00:00:01 Returning block of 1912789 for bucket 53 bucket 59: 20% Getting block 74 of 206 Reserving size (4338519) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: Getting block 75 of 206 Reserving size (4338519) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 58: 20% bucket 60: 20% Sorting block time: 00:00:01 Returning block of 3703483 for bucket 43 bucket 68: 10% Getting block 76 of 206 Reserving size (4338519) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 69: 10% bucket 70: 10% Sorting block time: 00:00:02 Returning block of 4190017 for bucket 45 bucket 63: 20% bucket 61: 20% bucket 56: 30% bucket 72: 10% bucket 55: 30% bucket 54: 100% Sorting block of length 3739645 for bucket 54 (Using difference cover) Getting block 77 of 206 Reserving size (4338519) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 57: 30% bucket 71: 10% bucket 62: 20% bucket 64: 20% bucket 65: 20% bucket 73: 10% Sorting block time: 00:00:02 Returning block of 4690483 for bucket 47 bucket 66: 20% Sorting block time: 00:00:02 Returning block of 4316825 for bucket 50 bucket 59: 30% Getting block 78 of 206 Reserving size (4338519) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 75: 10% bucket 67: 20% Getting block 79 of 206 Reserving size (4338519) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 74: 10% bucket 60: 30% bucket 58: 30% bucket 68: 20% bucket 76: 10% bucket 69: 20% bucket 70: 20% bucket 63: 30% bucket 56: 40% bucket 72: 20% bucket 61: 30% bucket 55: 40% bucket 57: 40% bucket 77: 10% bucket 62: 30% bucket 64: 30% Sorting block time: 00:00:02 Returning block of 4034067 for bucket 52 bucket 71: 20% bucket 65: 30% bucket 73: 20% bucket 66: 30% Getting block 80 of 206 Reserving size (4338519) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 59: 40% bucket 75: 20% bucket 67: 30% bucket 78: 10% bucket 79: 10% bucket 60: 40% bucket 74: 20% bucket 58: 40% bucket 68: 30% bucket 56: 50% bucket 76: 20% bucket 63: 40% bucket 70: 30% bucket 57: 50% Sorting block time: 00:00:01 Returning block of 3739646 for bucket 54 bucket 55: 50% bucket 61: 40% bucket 69: 30% bucket 72: 30% bucket 64: 40% bucket 62: 40% bucket 77: 20% Getting block 81 of 206 Reserving size (4338519) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 71: 30% bucket 73: 30% bucket 65: 40% bucket 66: 40% bucket 59: 50% bucket 75: 30% bucket 67: 40% bucket 80: 10% bucket 60: 50% bucket 79: 20% bucket 58: 50% bucket 74: 30% bucket 68: 40% bucket 78: 20% bucket 56: 60% bucket 76: 30% bucket 57: 60% bucket 63: 50% bucket 70: 40% bucket 61: 50% bucket 64: 50% bucket 55: 60% bucket 62: 50% bucket 72: 40% bucket 69: 40% bucket 77: 30% bucket 81: 10% bucket 71: 40% bucket 73: 40% bucket 66: 50% bucket 65: 50% bucket 75: 40% bucket 67: 50% bucket 60: 60% bucket 59: 60% bucket 58: 60% bucket 79: 30% bucket 80: 20% bucket 74: 40% bucket 56: 70% bucket 68: 50% bucket 57: 70% bucket 76: 40% bucket 63: 60% bucket 70: 50% bucket 78: 30% bucket 61: 60% bucket 64: 60% bucket 62: 60% bucket 69: 50% bucket 77: 40% bucket 55: 70% bucket 72: 50% bucket 71: 50% bucket 81: 20% bucket 73: 50% bucket 66: 60% bucket 65: 60% bucket 75: 50% bucket 67: 60% bucket 60: 70% bucket 58: 70% bucket 59: 70% bucket 79: 40% bucket 56: 80% bucket 74: 50% bucket 80: 30% bucket 68: 60% bucket 57: 80% bucket 76: 50% bucket 63: 70% bucket 70: 60% bucket 64: 70% bucket 62: 70% bucket 78: 40% bucket 69: 60% bucket 55: 80% bucket 61: 70% bucket 77: 50% bucket 72: 60% bucket 71: 60% bucket 66: 70% bucket 67: 70% bucket 60: 80% bucket 73: 60% bucket 65: 70% bucket 81: 30% bucket 58: 80% bucket 59: 80% bucket 75: 60% bucket 79: 50% bucket 56: 90% bucket 74: 60% bucket 57: 90% bucket 68: 70% bucket 80: 40% bucket 76: 60% bucket 63: 80% bucket 70: 70% bucket 64: 80% bucket 62: 80% bucket 77: 60% bucket 55: 90% bucket 69: 70% bucket 61: 80% bucket 78: 50% bucket 71: 70% bucket 66: 80% bucket 67: 80% bucket 72: 70% bucket 58: 90% bucket 59: 90% bucket 60: 90% bucket 56: 100% Sorting block of length 1701439 for bucket 56 (Using difference cover) bucket 75: 70% bucket 79: 60% bucket 65: 80% bucket 73: 70% bucket 57: 100% Sorting block of length 4078520 for bucket 57 (Using difference cover) bucket 81: 40% bucket 74: 70% bucket 68: 80% bucket 63: 90% bucket 76: 70% bucket 80: 50% bucket 64: 90% bucket 70: 80% bucket 62: 90% bucket 61: 90% bucket 77: 70% bucket 69: 80% bucket 55: 100% Sorting block of length 3228303 for bucket 55 (Using difference cover) bucket 78: 60% Sorting block time: 00:00:01 Returning block of 1701440 for bucket 56 bucket 67: 90% bucket 66: 90% bucket 58: 100% Sorting block of length 4191920 for bucket 58 (Using difference cover) Getting block 82 of 206 Reserving size (4338519) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 71: 80% bucket 60: 100% Sorting block of length 1688138 for bucket 60 (Using difference cover) bucket 59: 100% Sorting block of length 4109069 for bucket 59 (Using difference cover) bucket 79: 70% bucket 75: 80% bucket 72: 80% bucket 73: 80% bucket 65: 90% bucket 74: 80% bucket 81: 50% bucket 68: 90% bucket 63: 100% Sorting block of length 4236158 for bucket 63 (Using difference cover) bucket 76: 80% bucket 64: 100% Sorting block of length 2595066 for bucket 64 (Using difference cover) bucket 80: 60% bucket 70: 90% bucket 62: 100% Sorting block of length 4233080 for bucket 62 (Using difference cover) bucket 61: 100% Sorting block of length 3918833 for bucket 61 (Using difference cover) bucket 77: 80% bucket 69: 90% Sorting block time: 00:00:01 Returning block of 1688139 for bucket 60 bucket 78: 70% Getting block 83 of 206 Reserving size (4338519) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 67: 100% Sorting block of length 1466454 for bucket 67 (Using difference cover) bucket 66: 100% Sorting block of length 3940151 for bucket 66 (Using difference cover) bucket 82: 10% bucket 71: 90% bucket 75: 90% bucket 79: 80% bucket 72: 90% Sorting block time: 00:00:02 Returning block of 4078521 for bucket 57 bucket 73: 90% bucket 65: 100% Sorting block of length 3154306 for bucket 65 (Using difference cover) bucket 74: 90% Getting block 84 of 206 Reserving size (4338519) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: bucket 68: 100% Sorting block of length 3292555 for bucket 68 (Using difference cover) bucket 81: 60% bucket 76: 90% Sorting block time: 00:00:01 Returning block of 3228304 for bucket 55 bucket 80: 70% Getting block 85 of 206 Reserving size (4338519) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 70: 100% Sorting block of length 3624758 for bucket 70 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1466455 for bucket 67 Getting block 86 of 206 Reserving size (4338519) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: Sorting block time: 00:00:01 Returning block of 2595067 for bucket 64 bucket 77: 90% Getting block 87 of 206 Reserving size (4338519) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: bucket 69: 100% Sorting block of length 3623933 for bucket 69 (Using difference cover) bucket 78: 80% bucket 83: 10% bucket 82: 20% Sorting block time: 00:00:02 Returning block of 4191921 for bucket 58 bucket 71: 100% Sorting block of length 3768615 for bucket 71 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4109070 for bucket 59 bucket 79: 90% bucket 75: 100% Sorting block of length 1950123 for bucket 75 (Using difference cover) bucket 72: 100% Sorting block of length 1274606 for bucket 72 (Using difference cover) Getting block 88 of 206 Reserving size (4338519) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: Getting block 89 of 206 Reserving size (4338519) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: bucket 73: 100% Sorting block of length 3463397 for bucket 73 (Using difference cover) bucket 84: 10% bucket 74: 100% Sorting block of length 3386601 for bucket 74 (Using difference cover) bucket 81: 70% bucket 76: 100% Sorting block of length 3326191 for bucket 76 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4236159 for bucket 63 bucket 80: 80% Getting block 90 of 206 Reserving size (4338519) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: bucket 85: 10% Sorting block time: 00:00:02 Returning block of 3918834 for bucket 61 bucket 86: 10% Sorting block time: 00:00:02 Returning block of 3154307 for bucket 65 bucket 77: 100% Sorting block of length 1100303 for bucket 77 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4233081 for bucket 62 Getting block 91 of 206 Reserving size (4338519) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: Getting block 92 of 206 Reserving size (4338519) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: bucket 87: 10% Sorting block time: 00:00:01 Returning block of 1274607 for bucket 72 Getting block 93 of 206 Reserving size (4338519) for bucket 93 Calculating Z arrays for bucket 93 Entering block accumulator loop for bucket 93: Getting block 94 of 206 Reserving size (4338519) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 94: bucket 78: 90% bucket 83: 20% Sorting block time: 00:00:02 Returning block of 3292556 for bucket 68 Sorting block time: 00:00:02 Returning block of 3940152 for bucket 66 bucket 82: 30% Getting block 95 of 206 Reserving size (4338519) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: bucket 79: 100% Sorting block of length 1394416 for bucket 79 (Using difference cover) Getting block 96 of 206 Reserving size (4338519) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: bucket 88: 10% Sorting block time: 00:00:01 Returning block of 1950124 for bucket 75 bucket 89: 10% Getting block 97 of 206 Reserving size (4338519) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: bucket 84: 20% Sorting block time: 00:00:00 Returning block of 1100304 for bucket 77 bucket 81: 80% Getting block 98 of 206 Reserving size (4338519) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: Sorting block time: 00:00:01 Returning block of 3624759 for bucket 70 bucket 80: 90% Getting block 99 of 206 Reserving size (4338519) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: bucket 90: 10% bucket 85: 20% bucket 86: 20% Sorting block time: 00:00:01 Returning block of 3623934 for bucket 69 Sorting block time: 00:00:01 Returning block of 1394417 for bucket 79 Getting block 100 of 206 Reserving size (4338519) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: Getting block 101 of 206 Reserving size (4338519) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: bucket 91: 10% bucket 87: 20% bucket 92: 10% bucket 78: 100% Sorting block of length 3995521 for bucket 78 (Using difference cover) bucket 83: 30% bucket 93: 10% Sorting block time: 00:00:02 Returning block of 3463398 for bucket 73 Sorting block time: 00:00:02 Returning block of 3768616 for bucket 71 Sorting block time: 00:00:02 Returning block of 3386602 for bucket 74 Getting block 102 of 206 Reserving size (4338519) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: bucket 82: 40% Sorting block time: 00:00:02 Returning block of 3326192 for bucket 76 Getting block 103 of 206 Reserving size (4338519) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 95: 10% Getting block 104 of 206 Reserving size (4338519) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: bucket 88: 20% bucket 96: 10% bucket 84: 30% Getting block 105 of 206 Reserving size (4338519) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 89: 20% bucket 97: 10% bucket 81: 90% bucket 98: 10% bucket 94: 10% bucket 80: 100% Sorting block of length 3562904 for bucket 80 (Using difference cover) bucket 85: 30% bucket 86: 30% bucket 90: 20% bucket 99: 10% bucket 100: 10% bucket 91: 20% bucket 92: 20% bucket 93: 20% bucket 101: 10% bucket 87: 30% bucket 83: 40% bucket 102: 10% bucket 95: 20% bucket 88: 30% bucket 82: 50% bucket 84: 40% bucket 103: 10% bucket 96: 20% bucket 89: 30% bucket 104: 10% bucket 81: 100% Sorting block of length 2949121 for bucket 81 (Using difference cover) bucket 105: 10% bucket 97: 20% bucket 98: 20% bucket 85: 40% bucket 94: 20% bucket 90: 30% Sorting block time: 00:00:01 Returning block of 3995522 for bucket 78 bucket 86: 40% bucket 99: 20% Getting block 106 of 206 Reserving size (4338519) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: bucket 91: 30% bucket 92: 30% bucket 100: 20% bucket 93: 30% bucket 83: 50% bucket 82: 60% bucket 88: 40% bucket 101: 20% Sorting block time: 00:00:02 Returning block of 3562905 for bucket 80 bucket 95: 30% bucket 87: 40% bucket 102: 20% Getting block 107 of 206 Reserving size (4338519) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: bucket 105: 20% bucket 103: 20% bucket 84: 50% bucket 89: 40% bucket 104: 20% bucket 96: 30% bucket 97: 30% bucket 85: 50% bucket 98: 30% bucket 94: 30% bucket 90: 40% Sorting block time: 00:00:01 Returning block of 2949122 for bucket 81 bucket 106: 10% bucket 86: 50% Getting block 108 of 206 Reserving size (4338519) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 92: 40% bucket 91: 40% bucket 83: 60% bucket 100: 30% bucket 99: 30% bucket 82: 70% bucket 88: 50% bucket 105: 30% bucket 93: 40% bucket 87: 50% bucket 107: 10% bucket 84: 60% bucket 95: 40% bucket 101: 30% bucket 102: 30% bucket 104: 30% bucket 89: 50% bucket 96: 40% bucket 103: 30% bucket 97: 40% bucket 85: 60% bucket 94: 40% bucket 106: 20% bucket 90: 50% bucket 86: 60% bucket 98: 40% bucket 108: 10% bucket 83: 70% bucket 105: 40% bucket 91: 50% bucket 82: 80% bucket 92: 50% bucket 100: 40% bucket 88: 60% bucket 107: 20% bucket 87: 60% bucket 93: 50% bucket 84: 70% bucket 99: 40% bucket 104: 40% bucket 101: 40% bucket 102: 40% bucket 96: 50% bucket 95: 50% bucket 89: 60% bucket 97: 50% bucket 85: 70% bucket 106: 30% bucket 103: 40% bucket 90: 60% bucket 94: 50% bucket 86: 70% bucket 108: 20% bucket 105: 50% bucket 83: 80% bucket 82: 90% bucket 98: 50% bucket 107: 30% bucket 91: 60% bucket 88: 70% bucket 100: 50% bucket 84: 80% bucket 92: 60% bucket 87: 70% bucket 104: 50% bucket 93: 60% bucket 96: 60% bucket 99: 50% bucket 102: 50% bucket 101: 50% bucket 95: 60% bucket 106: 40% bucket 85: 80% bucket 89: 70% bucket 97: 60% bucket 108: 30% bucket 90: 70% bucket 86: 80% bucket 94: 60% bucket 105: 60% bucket 103: 50% bucket 83: 90% bucket 107: 40% bucket 82: 100% Sorting block of length 3702774 for bucket 82 (Using difference cover) bucket 88: 80% bucket 84: 90% bucket 91: 70% bucket 98: 60% bucket 87: 80% bucket 100: 60% bucket 92: 70% bucket 104: 60% bucket 106: 50% bucket 93: 70% bucket 96: 70% bucket 101: 60% bucket 99: 60% bucket 85: 90% bucket 102: 60% bucket 89: 80% bucket 108: 40% bucket 95: 70% bucket 105: 70% bucket 86: 90% bucket 90: 80% bucket 97: 70% bucket 94: 70% bucket 83: 100% Sorting block of length 3707790 for bucket 83 (Using difference cover) bucket 107: 50% bucket 103: 60% bucket 84: 100% Sorting block of length 3929364 for bucket 84 (Using difference cover) bucket 88: 90% bucket 91: 80% bucket 87: 90% bucket 100: 70% bucket 98: 70% bucket 92: 80% bucket 106: 60% bucket 104: 70% bucket 93: 80% bucket 96: 80% bucket 85: 100% Sorting block of length 4130050 for bucket 85 (Using difference cover) bucket 105: 80% bucket 108: 50% bucket 101: 70% Sorting block time: 00:00:02 Returning block of 3702775 for bucket 82 bucket 86: 100% Sorting block of length 2809169 for bucket 86 (Using difference cover) bucket 89: 90% bucket 90: 90% bucket 95: 80% bucket 99: 70% bucket 102: 70% bucket 107: 60% bucket 94: 80% Getting block 109 of 206 Reserving size (4338519) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 97: 80% bucket 103: 70% bucket 88: 100% Sorting block of length 2084618 for bucket 88 (Using difference cover) bucket 87: 100% Sorting block of length 2293145 for bucket 87 (Using difference cover) bucket 91: 90% bucket 100: 80% bucket 98: 80% bucket 106: 70% bucket 92: 90% bucket 104: 80% bucket 105: 90% bucket 108: 60% Exited Ebwt loop fchr[A]: 0 fchr[C]: 215403148 fchr[G]: 215403148 fchr[T]: 323920226 fchr[$]: 647885551 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 220173300 bytes to primary EBWT file: BS_CT.1.bt2 Wrote 161971392 bytes to secondary EBWT file: BS_CT.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 647885551 bwtLen: 647885552 sz: 161971388 bwtSz: 161971388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 40492847 offsSz: 161971388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3374404 numLines: 3374404 ebwtTotLen: 215961856 ebwtTotSz: 215961856 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:04:53 Reading reference sizes bucket 93: 90% bucket 96: 90% Sorting block time: 00:00:02 Returning block of 3707791 for bucket 83 bucket 89: 100% Sorting block of length 3138500 for bucket 89 (Using difference cover) bucket 90: 100% Sorting block of length 1518505 for bucket 90 (Using difference cover) bucket 107: 70% bucket 109: 10% bucket 101: 80% bucket 95: 90% Getting block 110 of 206 Reserving size (4338519) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 99: 80% bucket 94: 90% bucket 102: 80% Sorting block time: 00:00:02 Returning block of 3929365 for bucket 84 bucket 97: 90% Getting block 111 of 206 Reserving size (4338519) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: Sorting block time: 00:00:01 Returning block of 2809170 for bucket 86 Sorting block time: 00:00:01 Returning block of 2084619 for bucket 88 Getting block 112 of 206 Reserving size (4338519) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 103: 80% Getting block 113 of 206 Reserving size (4338519) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 91: 100% Sorting block of length 3841709 for bucket 91 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2293146 for bucket 87 bucket 106: 80% Getting block 114 of 206 Reserving size (4338519) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: bucket 105: 100% Sorting block of length 2003210 for bucket 105 (Using difference cover) bucket 100: 90% bucket 108: 70% bucket 92: 100% Sorting block of length 3791781 for bucket 92 (Using difference cover) bucket 98: 90% Sorting block time: 00:00:01 Returning block of 4130051 for bucket 85 bucket 104: 90% Getting block 115 of 206 Reserving size (4338519) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: Sorting block time: 00:00:00 Returning block of 1518506 for bucket 90 bucket 93: 100% Sorting block of length 2883858 for bucket 93 (Using difference cover) Getting block 116 of 206 Reserving size (4338519) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 109: 20% bucket 107: 80% bucket 96: 100% Sorting block of length 3907149 for bucket 96 (Using difference cover) bucket 95: 100% Sorting block of length 4213602 for bucket 95 (Using difference cover) bucket 110: 10% bucket 111: 10% bucket 101: 90% bucket 94: 100% Sorting block of length 3927995 for bucket 94 (Using difference cover) bucket 112: 10% bucket 97: 100% Sorting block of length 4045525 for bucket 97 (Using difference cover) bucket 113: 10% bucket 102: 90% bucket 99: 90% bucket 106: 90% bucket 103: 90% bucket 114: 10% Sorting block time: 00:00:01 Returning block of 3138501 for bucket 89 bucket 108: 80% Getting block 117 of 206 Reserving size (4338519) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: bucket 115: 10% bucket 104: 100% Sorting block of length 3551110 for bucket 104 (Using difference cover) bucket 98: 100% Sorting block of length 4152309 for bucket 98 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2003211 for bucket 105 Getting block 118 of 206 Reserving size (4338519) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 116: 10% bucket 100: 100% Sorting block of length 1896493 for bucket 100 (Using difference cover) bucket 109: 30% bucket 107: 90% bucket 110: 20% bucket 111: 20% bucket 112: 20% bucket 113: 20% Sorting block time: 00:00:01 Returning block of 2883859 for bucket 93 bucket 101: 100% Sorting block of length 3435468 for bucket 101 (Using difference cover) Getting block 119 of 206 Reserving size (4338519) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: bucket 106: 100% Sorting block of length 3542112 for bucket 106 (Using difference cover) bucket 102: 100% Sorting block of length 3764953 for bucket 102 (Using difference cover) bucket 99: 100% Sorting block of length 2451642 for bucket 99 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3841710 for bucket 91 bucket 114: 20% bucket 108: 90% Sorting block time: 00:00:02 Returning block of 3791782 for bucket 92 bucket 103: 100% Sorting block of length 1647215 for bucket 103 (Using difference cover) bucket 117: 10% Getting block 120 of 206 Reserving size (4338519) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: Getting block 121 of 206 Reserving size (4338519) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 116: 20% bucket 115: 20% bucket 118: 10% Sorting block time: 00:00:01 Returning block of 1896494 for bucket 100 bucket 109: 40% Getting block 122 of 206 Reserving size (4338519) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: bucket 107: 100% Sorting block of length 4253106 for bucket 107 (Using difference cover) bucket 110: 30% Sorting block time: 00:00:01 Returning block of 3907150 for bucket 96 bucket 112: 30% bucket 111: 30% bucket 113: 30% Getting block 123 of 206 Reserving size (4338519) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: Sorting block time: 00:00:02 Returning block of 4045526 for bucket 97 bucket 119: 10% Getting block 124 of 206 Reserving size (4338519) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 114: 30% Sorting block time: 00:00:02 Returning block of 3927996 for bucket 94 Sorting block time: 00:00:02 Returning block of 4213603 for bucket 95 bucket 108: 100% Sorting block of length 3251873 for bucket 108 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1647216 for bucket 103 Getting block 125 of 206 Reserving size (4338519) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Getting block 126 of 206 Reserving size (4338519) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: bucket 120: 10% bucket 117: 20% Sorting block time: 00:00:02 Returning block of 3551111 for bucket 104 Getting block 127 of 206 Reserving size (4338519) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 121: 10% bucket 116: 30% Sorting block time: 00:00:01 Returning block of 2451643 for bucket 99 Getting block 128 of 206 Reserving size (4338519) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: bucket 115: 30% bucket 118: 20% Getting block 129 of 206 Reserving size (4338519) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 109: 50% bucket 122: 10% bucket 110: 40% Sorting block time: 00:00:02 Returning block of 4152310 for bucket 98 bucket 112: 40% bucket 111: 40% Getting block 130 of 206 Reserving size (4338519) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 123: 10% bucket 113: 40% Sorting block time: 00:00:01 Returning block of 3435469 for bucket 101 Sorting block time: 00:00:01 Returning block of 3542113 for bucket 106 bucket 124: 10% Getting block 131 of 206 Reserving size (4338519) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: Getting block 132 of 206 Reserving size (4338519) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 119: 20% bucket 114: 40% bucket 125: 10% bucket 126: 10% Sorting block time: 00:00:02 Returning block of 3764954 for bucket 102 bucket 120: 20% bucket 127: 10% bucket 117: 30% Getting block 133 of 206 Reserving size (4338519) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 121: 20% bucket 128: 10% bucket 115: 40% bucket 109: 60% bucket 129: 10% bucket 118: 30% bucket 122: 20% bucket 116: 40% bucket 110: 50% bucket 112: 50% bucket 111: 50% bucket 123: 20% bucket 113: 50% Sorting block time: 00:00:01 Returning block of 3251874 for bucket 108 Sorting block time: 00:00:02 Returning block of 4253107 for bucket 107 bucket 130: 10% Getting block 134 of 206 Reserving size (4338519) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 124: 20% bucket 125: 20% bucket 114: 50% bucket 132: 10% bucket 126: 20% bucket 119: 30% bucket 131: 10% Time reading reference sizes: 00:00:05 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Getting block 135 of 206 Reserving size (4338519) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 127: 20% bucket 120: 30% bucket 117: 40% bucket 121: 30% bucket 133: 10% bucket 128: 20% bucket 109: 70% bucket 115: 50% bucket 122: 30% bucket 118: 40% bucket 116: 50% bucket 112: 60% bucket 111: 60% bucket 110: 60% bucket 129: 20% bucket 123: 30% bucket 113: 60% bucket 125: 30% bucket 114: 60% bucket 134: 10% bucket 124: 30% bucket 126: 30% bucket 132: 20% bucket 130: 20% bucket 119: 40% bucket 131: 20% bucket 127: 30% bucket 135: 10% bucket 121: 40% bucket 117: 50% bucket 120: 40% bucket 122: 40% bucket 128: 30% bucket 109: 80% bucket 115: 60% bucket 116: 60% bucket 118: 50% bucket 133: 20% bucket 112: 70% bucket 111: 70% bucket 110: 70% bucket 123: 40% bucket 129: 30% bucket 113: 70% bucket 125: 40% bucket 114: 70% bucket 126: 40% bucket 132: 30% bucket 124: 40% bucket 127: 40% bucket 119: 50% bucket 130: 30% bucket 134: 20% bucket 131: 30% bucket 121: 50% bucket 117: 60% bucket 122: 50% bucket 109: 90% bucket 128: 40% bucket 120: 50% bucket 115: 70% bucket 135: 20% bucket 116: 70% bucket 133: 30% bucket 112: 80% bucket 111: 80% bucket 123: 50% bucket 118: 60% bucket 110: 80% bucket 113: 80% bucket 125: 50% bucket 129: 40% bucket 114: 80% bucket 124: 50% bucket 132: 40% bucket 127: 50% bucket 119: 60% bucket 134: 30% bucket 126: 50% bucket 130: 40% bucket 121: 60% bucket 131: 40% bucket 122: 60% bucket 117: 70% bucket 109: 100% Sorting block of length 4032959 for bucket 109 (Using difference cover) bucket 128: 50% bucket 115: 80% bucket 120: 60% bucket 116: 80% bucket 135: 30% bucket 123: 60% bucket 112: 90% bucket 111: 90% bucket 110: 90% bucket 125: 60% bucket 133: 40% bucket 113: 90% bucket 118: 70% bucket 114: 90% bucket 129: 50% bucket 132: 50% bucket 127: 60% bucket 124: 60% bucket 126: 60% bucket 134: 40% bucket 121: 70% bucket 119: 70% bucket 122: 70% bucket 130: 50% bucket 131: 50% Time to join reference sequences: 00:00:02 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 5784692 Using parameters --bmax 4338519 --dcv 1024 Doing ahead-of-time memory usage test bucket 117: 80% bucket 128: 60% bucket 115: 90% bucket 123: 70% bucket 116: 90% bucket 112: 100% Sorting block of length 2887883 for bucket 112 (Using difference cover) bucket 120: 70% bucket 111: 100% Sorting block of length 2567725 for bucket 111 (Using difference cover) bucket 135: 40% bucket 125: 70% bucket 110: 100% Sorting block of length 2723453 for bucket 110 (Using difference cover) bucket 133: 50% bucket 114: 100% Sorting block of length 3210753 for bucket 114 (Using difference cover) bucket 113: 100% Sorting block of length 2896354 for bucket 113 (Using difference cover) bucket 118: 80% bucket 127: 70% bucket 124: 70% bucket 132: 60% bucket 121: 80% bucket 122: 80% bucket 129: 60% bucket 126: 70% bucket 119: 80% bucket 130: 60% bucket 134: 50% bucket 131: 60% Sorting block time: 00:00:02 Returning block of 4032960 for bucket 109 bucket 117: 90% bucket 128: 70% bucket 123: 80% bucket 115: 100% Sorting block of length 3550245 for bucket 115 (Using difference cover) Passed! Constructing with these parameters: --bmax 4338519 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime bucket 125: 80% Getting block 136 of 206 Reserving size (4338519) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 116: 100% Sorting block of length 1750509 for bucket 116 (Using difference cover) bucket 135: 50% bucket 133: 60% bucket 120: 80% Building sPrimeOrder V-Sorting samples bucket 118: 90% Sorting block time: 00:00:01 Returning block of 2567726 for bucket 111 bucket 124: 80% Getting block 137 of 206 Reserving size (4338519) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: bucket 127: 80% Sorting block time: 00:00:01 Returning block of 2723454 for bucket 110 Sorting block time: 00:00:01 Returning block of 2887884 for bucket 112 bucket 132: 70% bucket 122: 90% Getting block 138 of 206 Reserving size (4338519) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: bucket 121: 90% Getting block 139 of 206 Reserving size (4338519) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: bucket 126: 80% bucket 129: 70% bucket 119: 90% bucket 130: 70% bucket 131: 70% bucket 134: 60% Sorting block time: 00:00:02 Returning block of 2896355 for bucket 113 bucket 123: 90% Sorting block time: 00:00:02 Returning block of 3210754 for bucket 114 bucket 128: 80% bucket 117: 100% Sorting block of length 4176924 for bucket 117 (Using difference cover) bucket 136: 10% bucket 125: 90% Sorting block time: 00:00:01 Returning block of 1750510 for bucket 116 Getting block 140 of 206 Reserving size (4338519) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: Getting block 141 of 206 Reserving size (4338519) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 135: 60% bucket 133: 70% Getting block 142 of 206 Reserving size (4338519) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 120: 90% bucket 118: 100% Sorting block of length 1550331 for bucket 118 (Using difference cover) bucket 124: 90% bucket 127: 90% bucket 137: 10% bucket 122: 100% Sorting block of length 1828335 for bucket 122 (Using difference cover) bucket 121: 100% Sorting block of length 4250351 for bucket 121 (Using difference cover) bucket 132: 80% bucket 126: 90% bucket 139: 10% Sorting block time: 00:00:01 Returning block of 3550246 for bucket 115 bucket 129: 80% bucket 130: 80% bucket 138: 10% bucket 119: 100% Sorting block of length 3987832 for bucket 119 (Using difference cover) bucket 131: 80% bucket 134: 70% bucket 123: 100% Sorting block of length 3495625 for bucket 123 (Using difference cover) Getting block 143 of 206 Reserving size (4338519) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 128: 90% bucket 125: 100% Sorting block of length 2980212 for bucket 125 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1550332 for bucket 118 bucket 133: 80% bucket 135: 70% Getting block 144 of 206 Reserving size (4338519) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 141: 10% bucket 120: 100% Sorting block of length 3251994 for bucket 120 (Using difference cover) bucket 124: 100% Sorting block of length 1973098 for bucket 124 (Using difference cover) bucket 140: 10% bucket 142: 10% bucket 136: 20% Sorting block time: 00:00:01 Returning block of 1828336 for bucket 122 bucket 126: 100% Sorting block of length 2989204 for bucket 126 (Using difference cover) bucket 137: 20% bucket 127: 100% Sorting block of length 4042561 for bucket 127 (Using difference cover) bucket 132: 90% Getting block 145 of 206 Reserving size (4338519) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 129: 90% bucket 130: 90% bucket 131: 90% bucket 134: 80% bucket 139: 20% bucket 143: 10% bucket 128: 100% Sorting block of length 3174876 for bucket 128 (Using difference cover) bucket 133: 90% Sorting block time: 00:00:02 Returning block of 4176925 for bucket 117 bucket 138: 20% bucket 144: 10% bucket 141: 20% bucket 135: 80% Sorting block time: 00:00:01 Returning block of 1973099 for bucket 124 Getting block 146 of 206 Reserving size (4338519) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 140: 20% Getting block 147 of 206 Reserving size (4338519) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 136: 30% bucket 142: 20% bucket 137: 30% bucket 132: 100% Sorting block of length 3486444 for bucket 132 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2980213 for bucket 125 Sorting block time: 00:00:01 Returning block of 3495626 for bucket 123 Getting block 148 of 206 Reserving size (4338519) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 129: 100% Sorting block of length 4278285 for bucket 129 (Using difference cover) Getting block 149 of 206 Reserving size (4338519) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 134: 90% bucket 130: 100% Sorting block of length 4080565 for bucket 130 (Using difference cover) bucket 131: 100% Sorting block of length 2105642 for bucket 131 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4250352 for bucket 121 Sorting block time: 00:00:01 Returning block of 3987833 for bucket 119 bucket 145: 10% Getting block 150 of 206 Reserving size (4338519) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: Getting block 151 of 206 Reserving size (4338519) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: Sorting block time: 00:00:01 Returning block of 3251995 for bucket 120 bucket 139: 30% bucket 143: 20% bucket 133: 100% Sorting block of length 2564582 for bucket 133 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2989205 for bucket 126 Getting block 152 of 206 Reserving size (4338519) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: Getting block 153 of 206 Reserving size (4338519) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 141: 30% bucket 135: 90% bucket 138: 30% bucket 144: 20% bucket 140: 30% bucket 146: 10% bucket 136: 40% bucket 137: 40% bucket 142: 30% Sorting block time: 00:00:02 Returning block of 4042562 for bucket 127 bucket 147: 10% Sorting block time: 00:00:01 Returning block of 3174877 for bucket 128 bucket 148: 10% bucket 134: 100% Sorting block of length 2931538 for bucket 134 (Using difference cover) Getting block 154 of 206 Reserving size (4338519) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: Getting block 155 of 206 Reserving size (4338519) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 149: 10% bucket 145: 20% Sorting block time: 00:00:01 Returning block of 2105643 for bucket 131 bucket 150: 10% bucket 143: 30% Getting block 156 of 206 Reserving size (4338519) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 151: 10% bucket 139: 40% bucket 135: 100% Sorting block of length 3808264 for bucket 135 (Using difference cover) bucket 153: 10% bucket 141: 40% Sorting block time: 00:00:01 Returning block of 3486445 for bucket 132 bucket 152: 10% bucket 136: 50% bucket 138: 40% Getting block 157 of 206 bucket 137: 50% Reserving size (4338519) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 140: 40% Sorting block time: 00:00:02 Returning block of 2564583 for bucket 133 bucket 144: 30% bucket 146: 20% Getting block 158 of 206 Reserving size (4338519) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: bucket 142: 40% bucket 154: 10% bucket 149: 20% bucket 147: 20% bucket 145: 30% bucket 148: 20% bucket 152: 20% bucket 143: 40% Sorting block time: 00:00:02 Returning block of 4080566 for bucket 130 bucket 155: 10% bucket 156: 10% Sorting block time: 00:00:02 Returning block of 2931539 for bucket 134 Getting block 159 of 206 Reserving size (4338519) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 151: 20% Sorting block time: 00:00:03 Returning block of 4278286 for bucket 129 bucket 150: 20% bucket 153: 20% Getting block 160 of 206 Reserving size (4338519) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 139: 50% bucket 141: 50% bucket 137: 60% bucket 136: 60% Getting block 161 of 206 Reserving size (4338519) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 140: 50% bucket 138: 50% bucket 157: 10% V-Sorting samples time: 00:00:06 Allocating rank array Ranking v-sort output bucket 158: 10% bucket 144: 40% bucket 154: 20% bucket 146: 30% bucket 147: 30% bucket 145: 40% bucket 149: 30% bucket 148: 30% bucket 142: 50% bucket 152: 30% bucket 143: 50% bucket 156: 20% bucket 155: 20% Sorting block time: 00:00:03 Returning block of 3808265 for bucket 135 bucket 159: 10% bucket 160: 10% bucket 151: 30% bucket 150: 30% bucket 139: 60% Getting block 162 of 206 Reserving size (4338519) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 153: 30% bucket 136: 70% bucket 141: 60% bucket 140: 60% bucket 137: 70% bucket 161: 10% bucket 138: 60% bucket 158: 20% bucket 144: 50% bucket 146: 40% bucket 157: 20% bucket 154: 30% bucket 147: 40% bucket 145: 50% bucket 149: 40% bucket 142: 60% bucket 152: 40% bucket 148: 40% bucket 156: 30% bucket 143: 60% bucket 151: 40% bucket 160: 20% bucket 162: 10% bucket 159: 20% bucket 150: 40% bucket 155: 30% bucket 139: 70% bucket 153: 40% bucket 136: 80% bucket 137: 80% bucket 141: 70% bucket 161: 20% bucket 140: 70% bucket 158: 30% bucket 146: 50% bucket 138: 70% bucket 144: 60% bucket 147: 50% bucket 154: 40% bucket 145: 60% bucket 157: 30% bucket 149: 50% bucket 142: 70% bucket 152: 50% bucket 162: 20% bucket 156: 40% bucket 143: 70% bucket 151: 50% bucket 160: 30% bucket 148: 50% bucket 159: 30% bucket 150: 50% bucket 139: 80% bucket 137: 90% bucket 153: 50% bucket 136: 90% bucket 155: 40% bucket 161: 30% bucket 141: 80% bucket 158: 40% bucket 140: 80% bucket 146: 60% bucket 144: 70% bucket 147: 60% bucket 138: 80% bucket 157: 40% bucket 145: 70% bucket 149: 60% bucket 154: 50% bucket 142: 80% bucket 152: 60% bucket 162: 30% bucket 151: 60% bucket 156: 50% bucket 160: 40% bucket 143: 80% Ranking v-sort output time: 00:00:03 Invoking Larsson-Sadakane on ranks bucket 159: 40% bucket 148: 60% bucket 139: 90% bucket 150: 60% bucket 136: 100% Sorting block of length 3299917 for bucket 136 (Using difference cover) bucket 153: 60% bucket 137: 100% Sorting block of length 2521687 for bucket 137 (Using difference cover) bucket 141: 90% bucket 161: 40% bucket 155: 50% bucket 158: 50% bucket 140: 90% bucket 144: 80% bucket 146: 70% bucket 147: 70% bucket 157: 50% bucket 138: 90% bucket 145: 80% bucket 149: 70% bucket 154: 60% bucket 142: 90% bucket 152: 70% bucket 162: 40% bucket 156: 60% bucket 160: 50% bucket 148: 70% bucket 151: 70% bucket 150: 70% bucket 139: 100% Sorting block of length 4167391 for bucket 139 (Using difference cover) bucket 159: 50% bucket 143: 90% bucket 153: 70% bucket 141: 100% Sorting block of length 3152187 for bucket 141 (Using difference cover) bucket 161: 50% bucket 155: 60% bucket 140: 100% Sorting block of length 1689222 for bucket 140 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2521688 for bucket 137 bucket 158: 60% bucket 144: 90% Getting block 163 of 206 Reserving size (4338519) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: bucket 146: 80% bucket 147: 80% Sorting block time: 00:00:02 Returning block of 3299918 for bucket 136 bucket 157: 60% bucket 149: 80% Getting block 164 of 206 Reserving size (4338519) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: bucket 154: 70% bucket 145: 90% bucket 142: 100% Sorting block of length 2739474 for bucket 142 (Using difference cover) bucket 138: 100% Sorting block of length 4083589 for bucket 138 (Using difference cover) bucket 162: 50% bucket 152: 80% bucket 160: 60% bucket 156: 70% bucket 151: 80% bucket 148: 80% bucket 150: 80% bucket 159: 60% bucket 153: 80% bucket 161: 60% Sorting block time: 00:00:01 Returning block of 1689223 for bucket 140 Getting block 165 of 206 Reserving size (4338519) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 143: 100% Sorting block of length 3060874 for bucket 143 (Using difference cover) bucket 155: 70% bucket 158: 70% bucket 163: 10% bucket 144: 100% Sorting block of length 3034574 for bucket 144 (Using difference cover) bucket 146: 90% bucket 147: 90% bucket 157: 70% bucket 164: 10% bucket 154: 80% bucket 149: 90% bucket 145: 100% Sorting block of length 3964227 for bucket 145 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3152188 for bucket 141 bucket 162: 60% Getting block 166 of 206 Reserving size (4338519) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 152: 90% bucket 160: 70% bucket 148: 90% bucket 156: 80% bucket 151: 90% bucket 150: 90% bucket 159: 70% Sorting block time: 00:00:01 Returning block of 2739475 for bucket 142 bucket 153: 90% Sorting block time: 00:00:02 Returning block of 4167392 for bucket 139 bucket 161: 70% Getting block 167 of 206 Reserving size (4338519) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: bucket 165: 10% bucket 155: 80% bucket 158: 80% bucket 163: 20% Getting block 168 of 206 Reserving size (4338519) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 147: 100% Sorting block of length 3970624 for bucket 147 (Using difference cover) bucket 146: 100% Sorting block of length 3482644 for bucket 146 (Using difference cover) bucket 164: 20% bucket 157: 80% bucket 154: 90% bucket 149: 100% Sorting block of length 2238596 for bucket 149 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4083590 for bucket 138 Sorting block time: 00:00:02 Returning block of 3060875 for bucket 143 bucket 162: 70% bucket 166: 10% Getting block 169 of 206 Reserving size (4338519) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 152: 100% Sorting block of length 1352538 for bucket 152 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3034575 for bucket 144 Getting block 170 of 206 Reserving size (4338519) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 160: 80% bucket 148: 100% Sorting block of length 2537711 for bucket 148 (Using difference cover) bucket 151: 100% Sorting block of length 3965167 for bucket 151 (Using difference cover) bucket 156: 90% Getting block 171 of 206 Reserving size (4338519) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 150: 100% Sorting block of length 2408299 for bucket 150 (Using difference cover) bucket 153: 100% Sorting block of length 3753827 for bucket 153 (Using difference cover) bucket 159: 80% bucket 161: 80% bucket 165: 20% bucket 167: 10% bucket 163: 30% bucket 158: 90% bucket 168: 10% bucket 155: 90% bucket 164: 30% bucket 157: 90% Sorting block time: 00:00:01 Returning block of 3964228 for bucket 145 bucket 154: 100% Sorting block of length 1413817 for bucket 154 (Using difference cover) Getting block 172 of 206 Reserving size (4338519) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: Sorting block time: 00:00:01 Returning block of 1352539 for bucket 152 Sorting block time: 00:00:01 Returning block of 2238597 for bucket 149 bucket 166: 20% Getting block 173 of 206 Reserving size (4338519) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 169: 10% Getting block 174 of 206 Reserving size (4338519) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 170: 10% bucket 160: 90% bucket 162: 80% bucket 156: 100% Sorting block of length 2289647 for bucket 156 (Using difference cover) bucket 171: 10% bucket 165: 30% bucket 161: 90% bucket 159: 90% Sorting block time: 00:00:02 Returning block of 3482645 for bucket 146 Sorting block time: 00:00:01 Returning block of 2537712 for bucket 148 bucket 167: 20% bucket 163: 40% Sorting block time: 00:00:01 Returning block of 2408300 for bucket 150 Getting block 175 of 206 Reserving size (4338519) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: Getting block 176 of 206 Reserving size (4338519) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 168: 20% Getting block 177 of 206 Reserving size (4338519) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: Sorting block time: 00:00:01 Returning block of 1413818 for bucket 154 bucket 158: 100% Sorting block of length 4236834 for bucket 158 (Using difference cover) bucket 155: 100% Sorting block of length 4185525 for bucket 155 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3970625 for bucket 147 Getting block 178 of 206 Reserving size (4338519) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 164: 40% Getting block 179 of 206 Reserving size (4338519) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 157: 100% Sorting block of length 3569961 for bucket 157 (Using difference cover) bucket 166: 30% bucket 173: 10% bucket 169: 20% bucket 174: 10% bucket 170: 20% Sorting block time: 00:00:02 Returning block of 3753828 for bucket 153 bucket 162: 90% bucket 160: 100% Sorting block of length 1173965 for bucket 160 (Using difference cover) bucket 172: 10% Getting block 180 of 206 Reserving size (4338519) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 171: 20% Sorting block time: 00:00:02 Returning block of 3965168 for bucket 151 bucket 165: 40% bucket 161: 100% Sorting block of length 4260307 for bucket 161 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2289648 for bucket 156 Getting block 181 of 206 Reserving size (4338519) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 175: 10% bucket 163: 50% bucket 176: 10% Getting block 182 of 206 Reserving size (4338519) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 167: 30% bucket 177: 10% bucket 168: 30% bucket 159: 100% Sorting block of length 4191503 for bucket 159 (Using difference cover) bucket 164: 50% bucket 179: 10% Sorting block time: 00:00:00 Returning block of 1173966 for bucket 160 Getting block 183 of 206 Reserving size (4338519) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: Invoking Larsson-Sadakane on ranks time: 00:00:06 Sanity-checking and returning Building samples Reserving space for 300 sample suffixes Generating random suffixes QSorting 300 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 300 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes bucket 178: 10% bucket 166: 40% bucket 174: 20% bucket 169: 30% bucket 171: 30% bucket 173: 20% bucket 170: 30% bucket 162: 100% Sorting block of length 351649 for bucket 162 (Using difference cover) bucket 165: 50% bucket 180: 10% bucket 182: 10% Sorting block time: 00:00:00 Returning block of 351650 for bucket 162 bucket 168: 40% Getting block 184 of 206 Reserving size (4338519) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: bucket 163: 60% bucket 176: 20% bucket 164: 60% Sorting block time: 00:00:02 Returning block of 4185526 for bucket 155 bucket 172: 20% Sorting block time: 00:00:02 Returning block of 3569962 for bucket 157 bucket 175: 20% Getting block 185 of 206 Reserving size (4338519) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: Getting block 186 of 206 Reserving size (4338519) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: bucket 167: 40% bucket 181: 10% bucket 177: 20% bucket 170: 40% bucket 180: 20% bucket 179: 20% bucket 164: 70% bucket 182: 20% bucket 171: 40% bucket 165: 60% bucket 166: 50% bucket 183: 10% bucket 169: 40% bucket 174: 30% bucket 178: 20% bucket 173: 30% Sorting block time: 00:00:03 Returning block of 4236835 for bucket 158 bucket 168: 50% bucket 175: 30% bucket 185: 10% bucket 176: 30% Getting block 187 of 206 Reserving size (4338519) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: bucket 163: 70% bucket 170: 50% bucket 172: 30% bucket 186: 10% bucket 167: 50% bucket 184: 10% bucket 180: 30% Sorting block time: 00:00:03 Returning block of 4260308 for bucket 161 bucket 169: 50% bucket 181: 20% bucket 177: 30% bucket 182: 30% bucket 179: 30% bucket 178: 30% Getting block 188 of 206 Reserving size (4338519) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 164: 80% bucket 175: 40% bucket 165: 70% bucket 166: 60% bucket 183: 20% bucket 186: 20% bucket 170: 60% bucket 174: 40% Sorting block time: 00:00:04 Returning block of 4191504 for bucket 159 bucket 167: 60% bucket 187: 10% bucket 185: 20% bucket 173: 40% bucket 168: 60% bucket 176: 40% bucket 171: 50% bucket 163: 80% Getting block 189 of 206 Reserving size (4338519) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 180: 40% bucket 165: 80% bucket 186: 30% bucket 169: 60% bucket 172: 40% bucket 181: 30% bucket 175: 50% bucket 164: 90% bucket 182: 40% bucket 184: 20% bucket 179: 40% bucket 177: 40% bucket 168: 70% bucket 166: 70% bucket 176: 50% bucket 170: 70% bucket 167: 70% bucket 183: 30% bucket 178: 40% bucket 180: 50% bucket 188: 10% bucket 187: 20% bucket 185: 30% bucket 163: 90% bucket 174: 50% bucket 173: 50% bucket 175: 60% Splitting and merging Splitting and merging time: 00:00:00 Split 35, merged 130; iterating... bucket 165: 90% bucket 171: 60% bucket 182: 50% bucket 186: 40% bucket 179: 50% bucket 189: 10% bucket 181: 40% bucket 164: 100% Sorting block of length 3647893 for bucket 164 (Using difference cover) bucket 184: 30% bucket 168: 80% bucket 166: 80% bucket 176: 60% bucket 183: 40% bucket 177: 50% bucket 172: 50% bucket 167: 80% bucket 180: 60% bucket 170: 80% bucket 169: 70% bucket 188: 20% bucket 175: 70% bucket 185: 40% bucket 178: 50% bucket 174: 60% bucket 163: 100% Sorting block of length 4094153 for bucket 163 (Using difference cover) bucket 171: 70% bucket 187: 30% bucket 184: 40% bucket 173: 60% bucket 186: 50% bucket 182: 60% bucket 179: 60% bucket 189: 20% bucket 165: 100% Sorting block of length 4002292 for bucket 165 (Using difference cover) bucket 181: 50% bucket 183: 50% bucket 168: 90% bucket 176: 70% bucket 177: 60% bucket 166: 90% bucket 180: 70% bucket 167: 90% bucket 172: 60% bucket 171: 80% bucket 169: 80% bucket 173: 70% bucket 170: 90% bucket 188: 30% bucket 175: 80% bucket 178: 60% bucket 185: 50% bucket 186: 60% bucket 183: 60% bucket 174: 70% bucket 189: 30% bucket 187: 40% Sorting block time: 00:00:03 Returning block of 3647894 for bucket 164 bucket 184: 50% bucket 179: 70% Getting block 190 of 206 Reserving size (4338519) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 182: 70% bucket 180: 80% bucket 181: 60% bucket 176: 80% bucket 177: 70% bucket 168: 100% Sorting block of length 3203836 for bucket 168 (Using difference cover) bucket 172: 70% bucket 188: 40% bucket 166: 100% Sorting block of length 3482912 for bucket 166 (Using difference cover) bucket 171: 90% bucket 173: 80% bucket 167: 100% Sorting block of length 4277286 for bucket 167 (Using difference cover) bucket 189: 40% bucket 169: 90% bucket 170: 100% Sorting block of length 2620153 for bucket 170 (Using difference cover) bucket 185: 60% bucket 183: 70% bucket 174: 80% bucket 184: 60% bucket 186: 70% bucket 175: 90% bucket 178: 70% bucket 187: 50% bucket 179: 80% bucket 190: 10% Sorting block time: 00:00:03 Returning block of 4002293 for bucket 165 Splitting and merging Splitting and merging time: 00:00:00 Split 18, merged 14; iterating... bucket 181: 70% bucket 180: 90% Getting block 191 of 206 Reserving size (4338519) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: bucket 182: 80% bucket 172: 80% bucket 177: 80% Sorting block time: 00:00:04 Returning block of 4094154 for bucket 163 Getting block 192 of 206 Reserving size (4338519) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 188: 50% bucket 171: 100% Sorting block of length 2385354 for bucket 171 (Using difference cover) bucket 176: 90% bucket 189: 50% bucket 173: 90% bucket 169: 100% Sorting block of length 2233109 for bucket 169 (Using difference cover) bucket 183: 80% bucket 185: 70% bucket 174: 90% bucket 175: 100% Sorting block of length 2622331 for bucket 175 (Using difference cover) bucket 187: 60% bucket 178: 80% bucket 186: 80% bucket 184: 70% bucket 190: 20% bucket 179: 90% bucket 180: 100% Sorting block of length 4303369 for bucket 180 (Using difference cover) bucket 177: 90% Sorting block time: 00:00:02 Returning block of 2620154 for bucket 170 Sorting block time: 00:00:02 Returning block of 3203837 for bucket 168 bucket 182: 90% Getting block 193 of 206 Reserving size (4338519) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: Getting block 194 of 206 Reserving size (4338519) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 191: 10% bucket 181: 80% bucket 172: 90% bucket 192: 10% Sorting block time: 00:00:03 Returning block of 3482913 for bucket 166 bucket 176: 100% Sorting block of length 3582115 for bucket 176 (Using difference cover) Getting block 195 of 206 Reserving size (4338519) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 188: 60% bucket 189: 60% bucket 173: 100% Sorting block of length 3468091 for bucket 173 (Using difference cover) Sorting block time: 00:00:03 Returning block of 4277287 for bucket 167 bucket 185: 80% bucket 182: 100% Sorting block of length 4019852 for bucket 182 (Using difference cover) bucket 174: 100% Sorting block of length 2920680 for bucket 174 (Using difference cover) bucket 183: 90% Sorting block time: 00:00:02 Returning block of 2233110 for bucket 169 Getting block 196 of 206 Reserving size (4338519) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: bucket 187: 70% bucket 186: 90% Getting block 197 of 206 Reserving size (4338519) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 190: 30% bucket 184: 80% bucket 178: 90% Sorting block time: 00:00:02 Returning block of 2385355 for bucket 171 bucket 179: 100% Sorting block of length 4188995 for bucket 179 (Using difference cover) bucket 177: 100% Sorting block of length 2384757 for bucket 177 (Using difference cover) Getting block 198 of 206 Reserving size (4338519) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 193: 10% bucket 194: 10% bucket 191: 20% Sorting block time: 00:00:02 Returning block of 2622332 for bucket 175 Getting block 199 of 206 Reserving size (4338519) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 181: 90% bucket 192: 20% bucket 186: 100% Sorting block of length 3965474 for bucket 186 (Using difference cover) bucket 172: 100% Sorting block of length 2900859 for bucket 172 (Using difference cover) bucket 195: 10% bucket 188: 70% bucket 189: 70% bucket 190: 40% bucket 185: 90% bucket 196: 10% bucket 183: 100% Sorting block of length 2846050 for bucket 183 (Using difference cover) bucket 197: 10% bucket 178: 100% Sorting block of length 4061796 for bucket 178 (Using difference cover) bucket 184: 90% bucket 187: 80% bucket 193: 20% bucket 192: 30% bucket 194: 20% Sorting block time: 00:00:04 Returning block of 4303370 for bucket 180 bucket 198: 10% Splitting and merging Splitting and merging time: 00:00:00 Split 11, merged 9; iterating... bucket 199: 10% Sorting block time: 00:00:03 Returning block of 3582116 for bucket 176 Sorting block time: 00:00:02 Returning block of 2384758 for bucket 177 Getting block 200 of 206 Reserving size (4338519) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: Getting block 201 of 206 Reserving size (4338519) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: Sorting block time: 00:00:02 Returning block of 2920681 for bucket 174 bucket 191: 30% bucket 190: 50% Getting block 202 of 206 Reserving size (4338519) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: Getting block 203 of 206 Reserving size (4338519) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 189: 80% bucket 195: 20% Sorting block time: 00:00:03 Returning block of 3468092 for bucket 173 bucket 181: 100% Sorting block of length 3523196 for bucket 181 (Using difference cover) bucket 188: 80% Getting block 204 of 206 Reserving size (4338519) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 196: 20% bucket 185: 100% Sorting block of length 2390841 for bucket 185 (Using difference cover) bucket 197: 20% bucket 194: 30% Sorting block time: 00:00:03 Returning block of 4019853 for bucket 182 Sorting block time: 00:00:02 Returning block of 2900860 for bucket 172 Getting block 205 of 206 Reserving size (4338519) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: bucket 193: 30% bucket 184: 100% Sorting block of length 3489351 for bucket 184 (Using difference cover) Getting block 206 of 206 Reserving size (4338519) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 192: 40% bucket 190: 60% bucket 187: 90% bucket 199: 20% bucket 198: 20% bucket 200: 10% Sorting block time: 00:00:03 Returning block of 4188996 for bucket 179 Sorting block time: 00:00:02 Returning block of 3965475 for bucket 186 bucket 201: 10% bucket 202: 10% bucket 191: 40% bucket 189: 90% Sorting block time: 00:00:03 Returning block of 2846051 for bucket 183 bucket 195: 30% bucket 203: 10% bucket 188: 90% bucket 204: 10% bucket 206: 10% Sorting block time: 00:00:01 Returning block of 2390842 for bucket 185 bucket 197: 30% bucket 196: 30% bucket 194: 40% bucket 193: 40% bucket 190: 70% bucket 205: 10% bucket 192: 50% Sorting block time: 00:00:04 Returning block of 4061797 for bucket 178 bucket 199: 30% bucket 187: 100% Sorting block of length 3410524 for bucket 187 (Using difference cover) bucket 198: 30% bucket 191: 50% bucket 200: 20% bucket 201: 20% bucket 202: 20% Sorting block time: 00:00:03 Returning block of 3523197 for bucket 181 bucket 206: 20% bucket 189: 100% Sorting block of length 2940987 for bucket 189 (Using difference cover) bucket 203: 20% bucket 195: 40% bucket 193: 50% bucket 197: 40% bucket 188: 100% Sorting block of length 3784500 for bucket 188 (Using difference cover) bucket 190: 80% bucket 205: 20% bucket 204: 20% bucket 196: 40% bucket 194: 50% Sorting block time: 00:00:03 Returning block of 3489352 for bucket 184 bucket 202: 30% bucket 200: 30% bucket 192: 60% bucket 201: 30% bucket 206: 30% bucket 198: 40% bucket 191: 60% bucket 199: 40% Splitting and merging Splitting and merging time: 00:00:00 Split 7, merged 7; iterating... bucket 197: 50% bucket 203: 30% bucket 193: 60% bucket 196: 50% bucket 205: 30% bucket 190: 90% Sorting block time: 00:00:02 Returning block of 3410525 for bucket 187 bucket 195: 50% bucket 200: 40% bucket 194: 60% bucket 192: 70% bucket 206: 40% bucket 199: 50% bucket 197: 60% bucket 204: 30% Sorting block time: 00:00:01 Returning block of 3784501 for bucket 188 Sorting block time: 00:00:02 Returning block of 2940988 for bucket 189 bucket 202: 40% bucket 201: 40% bucket 203: 40% bucket 198: 50% bucket 206: 50% bucket 191: 70% bucket 196: 60% bucket 190: 100% Sorting block of length 3599429 for bucket 190 (Using difference cover) bucket 195: 60% bucket 193: 70% bucket 192: 80% bucket 205: 40% bucket 200: 50% bucket 197: 70% bucket 199: 60% bucket 194: 70% bucket 203: 50% bucket 198: 60% bucket 204: 40% bucket 206: 60% bucket 202: 50% bucket 201: 50% bucket 191: 80% bucket 205: 50% bucket 196: 70% bucket 192: 90% bucket 203: 60% bucket 195: 70% bucket 194: 80% bucket 199: 70% bucket 193: 80% bucket 200: 60% bucket 206: 70% bucket 197: 80% bucket 198: 70% bucket 204: 50% Sorting block time: 00:00:02 Returning block of 3599430 for bucket 190 bucket 201: 60% bucket 203: 70% bucket 205: 60% bucket 206: 80% bucket 202: 60% bucket 196: 80% bucket 191: 90% bucket 199: 80% bucket 195: 80% Splitting and merging Splitting and merging time: 00:00:00 Split 4, merged 6; iterating... Avg bucket size: 3.08517e+06 (target: 4338518) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 210 bucket 194: 90% Reserving size (4338519) for bucket 1 Getting block 2 of 210 Getting block 3 of 210 Getting block 4 of 210 Getting block 5 of 210 Getting block 6 of 210 Getting block 7 of 210 Getting block 8 of 210 Getting block 9 of 210 Getting block 10 of 210 Calculating Z arrays for bucket 1 Getting block 11 of 210 Getting block 12 of 210 Getting block 13 of 210 Getting block 14 of 210 Getting block 15 of 210 Getting block 16 of 210 Getting block 17 of 210 Getting block 18 of 210 Getting block 19 of 210 Getting block 20 of 210 Getting block 21 of 210 Getting block 22 of 210 Getting block 23 of 210 Getting block 24 of 210 Getting block 25 of 210 Getting block 26 of 210 bucket 193: 90% Reserving size (4338519) for bucket 2 Reserving size (4338519) for bucket 3 Reserving size (4338519) for bucket 4 Reserving size (4338519) for bucket 5 Reserving size (4338519) for bucket 6 Reserving size (4338519) for bucket 7 Reserving size (4338519) for bucket 8 Reserving size (4338519) for bucket 9 Reserving size (4338519) for bucket 10 Entering block accumulator loop for bucket 1: Reserving size (4338519) for bucket 11 Reserving size (4338519) for bucket 12 Reserving size (4338519) for bucket 13 Reserving size (4338519) for bucket 14 Reserving size (4338519) for bucket 15 Reserving size (4338519) for bucket 16 Reserving size (4338519) for bucket 17 Reserving size (4338519) for bucket 18 Reserving size (4338519) for bucket 19 Reserving size (4338519) for bucket 20 Reserving size (4338519) for bucket 21 Reserving size (4338519) for bucket 22 Reserving size (4338519) for bucket 23 Reserving size (4338519) for bucket 24 Reserving size (4338519) for bucket 25 Reserving size (4338519) for bucket 26 Calculating Z arrays for bucket 2 Calculating Z arrays for bucket 3 Calculating Z arrays for bucket 4 Calculating Z arrays for bucket 5 Calculating Z arrays for bucket 6 Calculating Z arrays for bucket 7 Calculating Z arrays for bucket 8 Calculating Z arrays for bucket 9 Calculating Z arrays for bucket 10 Calculating Z arrays for bucket 11 Calculating Z arrays for bucket 12 Calculating Z arrays for bucket 13 Calculating Z arrays for bucket 14 Calculating Z arrays for bucket 15 Calculating Z arrays for bucket 16 Calculating Z arrays for bucket 17 Calculating Z arrays for bucket 18 Calculating Z arrays for bucket 19 Calculating Z arrays for bucket 20 Calculating Z arrays for bucket 21 Calculating Z arrays for bucket 22 Calculating Z arrays for bucket 23 Calculating Z arrays for bucket 24 Calculating Z arrays for bucket 25 Calculating Z arrays for bucket 26 Entering block accumulator loop for bucket 2: Entering block accumulator loop for bucket 3: Entering block accumulator loop for bucket 6: Entering block accumulator loop for bucket 4: Entering block accumulator loop for bucket 7: Entering block accumulator loop for bucket 5: Entering block accumulator loop for bucket 9: Entering block accumulator loop for bucket 10: Entering block accumulator loop for bucket 8: Entering block accumulator loop for bucket 11: Entering block accumulator loop for bucket 13: Entering block accumulator loop for bucket 14: Entering block accumulator loop for bucket 12: Entering block accumulator loop for bucket 16: Entering block accumulator loop for bucket 17: Entering block accumulator loop for bucket 15: Entering block accumulator loop for bucket 18: Entering block accumulator loop for bucket 19: Entering block accumulator loop for bucket 20: Entering block accumulator loop for bucket 21: Entering block accumulator loop for bucket 23: Entering block accumulator loop for bucket 22: Entering block accumulator loop for bucket 24: Entering block accumulator loop for bucket 25: Entering block accumulator loop for bucket 26: bucket 192: 100% Sorting block of length 2287427 for bucket 192 (Using difference cover) Getting block 27 of 210 Reserving size (4338519) for bucket 27 Calculating Z arrays for bucket 27 Entering block accumulator loop for bucket 27: bucket 198: 80% bucket 200: 70% bucket 197: 90% bucket 204: 60% bucket 203: 80% bucket 205: 70% bucket 1: 10% bucket 7: 10% bucket 201: 70% bucket 5: 10% bucket 3: 10% bucket 206: 90% bucket 199: 90% bucket 8: 10% bucket 191: 100% Sorting block of length 2681498 for bucket 191 (Using difference cover) bucket 202: 70% bucket 195: 90% bucket 10: 10% bucket 194: 100% Sorting block of length 2540620 for bucket 194 (Using difference cover) bucket 12: 10% bucket 200: 80% bucket 2: 10% bucket 26: 10% bucket 24: 10% bucket 197: 100% Sorting block of length 2516072 for bucket 197 (Using difference cover) bucket 1: 20% bucket 4: 10% bucket 13: 10% bucket 6: 10% Sorting block time: 00:00:01 Returning block of 2287428 for bucket 192 bucket 11: 10% bucket 17: 10% bucket 15: 10% bucket 18: 10% bucket 19: 10% bucket 16: 10% bucket 5: 20% bucket 22: 10% bucket 21: 10% bucket 204: 70% bucket 14: 10% bucket 205: 80% bucket 25: 10% bucket 9: 10% bucket 193: 100% Sorting block of length 4305202 for bucket 193 (Using difference cover) bucket 8: 20% bucket 7: 20% bucket 27: 10% bucket 3: 20% bucket 12: 20% bucket 196: 90% bucket 23: 10% bucket 198: 90% bucket 10: 20% bucket 20: 10% bucket 203: 90% bucket 199: 100% Sorting block of length 3444204 for bucket 199 (Using difference cover) bucket 2: 20% bucket 1: 30% bucket 26: 20% bucket 202: 80% bucket 24: 20% bucket 206: 100% Sorting block of length 3632050 for bucket 206 (Using difference cover) bucket 200: 90% bucket 195: 100% Sorting block of length 1934516 for bucket 195 (Using difference cover) bucket 12: 30% bucket 7: 30% bucket 10: 30% bucket 201: 80% bucket 5: 30% bucket 18: 20% bucket 205: 90% bucket 4: 20% bucket 8: 30% bucket 2: 30% bucket 6: 20% bucket 15: 20% Sorting block time: 00:00:02 Returning block of 2540621 for bucket 194 Sorting block time: 00:00:01 Returning block of 2516073 for bucket 197 bucket 13: 20% bucket 14: 20% bucket 11: 20% bucket 203: 100% Sorting block of length 2968138 for bucket 203 (Using difference cover) bucket 17: 20% bucket 24: 30% bucket 22: 20% bucket 9: 20% bucket 26: 30% bucket 202: 90% bucket 19: 20% bucket 16: 20% bucket 3: 30% bucket 21: 20% bucket 200: 100% Sorting block of length 4185368 for bucket 200 (Using difference cover) bucket 1: 40% bucket 5: 40% bucket 23: 20% bucket 25: 20% bucket 27: 20% bucket 204: 80% bucket 12: 40% bucket 20: 20% bucket 18: 30% bucket 2: 40% bucket 4: 30% Sorting block time: 00:00:01 Returning block of 1934517 for bucket 195 bucket 205: 100% Sorting block of length 2737098 for bucket 205 (Using difference cover) Sorting block time: 00:00:03 Returning block of 2681499 for bucket 191 bucket 198: 100% Sorting block of length 2076818 for bucket 198 (Using difference cover) bucket 196: 100% Sorting block of length 3113038 for bucket 196 (Using difference cover) bucket 10: 40% bucket 9: 30% bucket 8: 40% bucket 13: 30% bucket 14: 30% bucket 7: 40% bucket 5: 50% bucket 15: 30% bucket 16: 30% bucket 11: 30% bucket 3: 40% bucket 22: 30% bucket 23: 30% bucket 12: 50% bucket 202: 100% Sorting block of length 4091644 for bucket 202 (Using difference cover) bucket 27: 30% bucket 4: 40% bucket 1: 50% bucket 6: 30% Sorting block time: 00:00:02 Returning block of 3444205 for bucket 199 bucket 24: 40% bucket 18: 40% bucket 2: 50% bucket 17: 30% bucket 25: 30% bucket 201: 90% bucket 26: 40% bucket 9: 40% bucket 21: 30% bucket 19: 30% bucket 8: 50% Sorting block time: 00:00:03 Returning block of 4305203 for bucket 193 Sorting block time: 00:00:02 Returning block of 2968139 for bucket 203 bucket 10: 50% bucket 11: 40% bucket 3: 50% bucket 5: 60% bucket 16: 40% bucket 1: 60% bucket 4: 50% bucket 20: 30% Sorting block time: 00:00:03 Returning block of 3632051 for bucket 206 bucket 7: 50% bucket 204: 90% bucket 12: 60% bucket 27: 40% bucket 14: 40% bucket 22: 40% Sorting block time: 00:00:01 Returning block of 2737099 for bucket 205 bucket 2: 60% bucket 17: 40% bucket 26: 50% bucket 24: 50% bucket 13: 40% bucket 9: 50% bucket 18: 50% Sorting block time: 00:00:01 Returning block of 2076819 for bucket 198 bucket 8: 60% bucket 6: 40% bucket 15: 40% bucket 3: 60% bucket 25: 40% bucket 23: 40% bucket 1: 70% bucket 5: 70% bucket 10: 60% bucket 201: 100% Sorting block of length 3710305 for bucket 201 (Using difference cover) bucket 12: 70% bucket 16: 50% bucket 4: 60% bucket 2: 70% bucket 27: 50% bucket 19: 40% bucket 21: 40% bucket 7: 60% Sorting block time: 00:00:03 Returning block of 4185369 for bucket 200 Sorting block time: 00:00:02 Returning block of 3113039 for bucket 196 bucket 204: 100% Sorting block of length 3018572 for bucket 204 (Using difference cover) bucket 9: 60% bucket 20: 40% bucket 26: 60% bucket 11: 50% bucket 8: 70% bucket 6: 50% bucket 24: 60% bucket 18: 60% bucket 14: 50% bucket 22: 50% bucket 1: 80% bucket 5: 80% bucket 17: 50% bucket 10: 70% bucket 23: 50% bucket 25: 50% bucket 3: 70% Sorting block time: 00:00:02 Returning block of 4091645 for bucket 202 bucket 12: 80% bucket 4: 70% bucket 2: 80% bucket 15: 50% bucket 13: 50% bucket 21: 50% bucket 9: 70% bucket 27: 60% bucket 8: 80% bucket 20: 50% bucket 1: 90% bucket 26: 70% bucket 14: 60% bucket 19: 50% bucket 18: 70% bucket 6: 60% bucket 24: 70% bucket 5: 90% bucket 17: 60% bucket 7: 70% bucket 10: 80% bucket 22: 60% bucket 16: 60% bucket 3: 80% bucket 11: 60% bucket 25: 60% bucket 23: 60% bucket 2: 90% bucket 12: 90% bucket 4: 80% bucket 15: 60% bucket 13: 60% bucket 9: 80% Sorting block time: 00:00:01 Returning block of 3018573 for bucket 204 bucket 8: 90% bucket 1: 100% Sorting block of length 4249819 for bucket 1 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3710306 for bucket 201 bucket 19: 60% bucket 21: 60% bucket 6: 70% bucket 18: 80% bucket 26: 80% bucket 20: 60% bucket 7: 80% bucket 14: 70% bucket 17: 70% bucket 5: 100% Sorting block of length 3399279 for bucket 5 (Using difference cover) bucket 3: 90% bucket 27: 70% bucket 10: 90% bucket 16: 70% bucket 24: 80% bucket 22: 70% bucket 11: 70% bucket 2: 100% Sorting block of length 2140557 for bucket 2 (Using difference cover) bucket 4: 90% bucket 23: 70% bucket 25: 70% bucket 12: 100% Sorting block of length 3155888 for bucket 12 (Using difference cover) bucket 15: 70% bucket 13: 70% bucket 9: 90% bucket 8: 100% Sorting block of length 3646992 for bucket 8 (Using difference cover) bucket 6: 80% bucket 19: 70% bucket 21: 70% bucket 3: 100% Sorting block of length 3640331 for bucket 3 (Using difference cover) bucket 7: 90% bucket 17: 80% bucket 14: 80% bucket 18: 90% bucket 20: 70% bucket 10: 100% Sorting block of length 3995233 for bucket 10 (Using difference cover) bucket 26: 90% bucket 16: 80% bucket 4: 100% Sorting block of length 1013351 for bucket 4 (Using difference cover) bucket 27: 80% bucket 22: 80% bucket 11: 80% bucket 24: 90% bucket 23: 80% bucket 25: 80% bucket 15: 80% bucket 13: 80% bucket 9: 100% Sorting block of length 3789127 for bucket 9 (Using difference cover) bucket 6: 90% Sorting block time: 00:00:00 Returning block of 1013352 for bucket 4 Sorting block time: 00:00:01 Returning block of 2140558 for bucket 2 Getting block 28 of 210 Reserving size (4338519) for bucket 28 Calculating Z arrays for bucket 28 Entering block accumulator loop for bucket 28: bucket 19: 80% bucket 7: 100% Sorting block of length 2826234 for bucket 7 (Using difference cover) bucket 21: 80% bucket 17: 90% Getting block 29 of 210 Reserving size (4338519) for bucket 29 Calculating Z arrays for bucket 29 Entering block accumulator loop for bucket 29: bucket 14: 90% bucket 18: 100% Sorting block of length 4235952 for bucket 18 (Using difference cover) bucket 20: 80% bucket 16: 90% bucket 26: 100% Sorting block of length 1655001 for bucket 26 (Using difference cover) bucket 11: 90% bucket 22: 90% bucket 27: 90% bucket 24: 100% Sorting block of length 3354239 for bucket 24 (Using difference cover) bucket 23: 90% bucket 25: 90% bucket 13: 90% bucket 15: 90% Sorting block time: 00:00:02 Returning block of 3399280 for bucket 5 bucket 6: 100% Sorting block of length 3441734 for bucket 6 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3155889 for bucket 12 Getting block 30 of 210 Reserving size (4338519) for bucket 30 Calculating Z arrays for bucket 30 Entering block accumulator loop for bucket 30: Sorting block time: 00:00:02 Returning block of 4249820 for bucket 1 Getting block 31 of 210 Reserving size (4338519) for bucket 31 Calculating Z arrays for bucket 31 Entering block accumulator loop for bucket 31: bucket 17: 100% Sorting block of length 917038 for bucket 17 (Using difference cover) bucket 19: 90% bucket 21: 90% bucket 28: 10% bucket 14: 100% Sorting block of length 3167638 for bucket 14 (Using difference cover) Getting block 32 of 210 Reserving size (4338519) for bucket 32 Calculating Z arrays for bucket 32 Entering block accumulator loop for bucket 32: bucket 29: 10% bucket 11: 100% Sorting block of length 2527507 for bucket 11 (Using difference cover) bucket 16: 100% Sorting block of length 4235338 for bucket 16 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3640332 for bucket 3 Sorting block time: 00:00:01 Returning block of 3646993 for bucket 8 Getting block 33 of 210 Reserving size (4338519) for bucket 33 Calculating Z arrays for bucket 33 Entering block accumulator loop for bucket 33: Getting block 34 of 210 Reserving size (4338519) for bucket 34 Calculating Z arrays for bucket 34 Entering block accumulator loop for bucket 34: bucket 20: 90% Sorting block time: 00:00:00 Returning block of 917039 for bucket 17 bucket 22: 100% Sorting block of length 3507835 for bucket 22 (Using difference cover) Getting block 35 of 210 Reserving size (4338519) for bucket 35 Calculating Z arrays for bucket 35 Entering block accumulator loop for bucket 35: Sorting block time: 00:00:00 Returning block of 1655002 for bucket 26 Getting block 36 of 210 Reserving size (4338519) for bucket 36 Calculating Z arrays for bucket 36 Entering block accumulator loop for bucket 36: Sorting block time: 00:00:02 Returning block of 2826235 for bucket 7 bucket 27: 100% Sorting block of length 3987710 for bucket 27 (Using difference cover) bucket 15: 100% Sorting block of length 1575321 for bucket 15 (Using difference cover) Getting block 37 of 210 Reserving size (4338519) for bucket 37 Calculating Z arrays for bucket 37 Entering block accumulator loop for bucket 37: Sorting block time: 00:00:02 Returning block of 3995234 for bucket 10 Getting block 38 of 210 Reserving size (4338519) for bucket 38 Calculating Z arrays for bucket 38 Entering block accumulator loop for bucket 38: Sorting block time: 00:00:02 Returning block of 3789128 for bucket 9 Getting block 39 of 210 Reserving size (4338519) for bucket 39 Calculating Z arrays for bucket 39 Entering block accumulator loop for bucket 39: bucket 30: 10% Sorting block time: 00:00:01 Returning block of 3354240 for bucket 24 Sorting block time: 00:00:01 Returning block of 2527508 for bucket 11 Getting block 40 of 210 Reserving size (4338519) for bucket 40 Calculating Z arrays for bucket 40 Entering block accumulator loop for bucket 40: Sorting block time: 00:00:01 Returning block of 3167639 for bucket 14 bucket 23: 100% Sorting block of length 3087165 for bucket 23 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3441735 for bucket 6 Sorting block time: 00:00:02 Returning block of 4235953 for bucket 18 Getting block 41 of 210 Reserving size (4338519) for bucket 41 Calculating Z arrays for bucket 41 Entering block accumulator loop for bucket 41: Sorting block time: 00:00:00 Returning block of 1575322 for bucket 15 Getting block 42 of 210 Reserving size (4338519) for bucket 42 Calculating Z arrays for bucket 42 Entering block accumulator loop for bucket 42: Exited Ebwt loop fchr[A]: 0 fchr[C]: 323920226 fchr[G]: 432422725 fchr[T]: 432422725 fchr[$]: 647885551 Getting block 43 of 210 Reserving size (4338519) for bucket 43 Calculating Z arrays for bucket 43 Entering block accumulator loop for bucket 43: Getting block 44 of 210 Reserving size (4338519) for bucket 44 Calculating Z arrays for bucket 44 Entering block accumulator loop for bucket 44: Exiting Ebwt::buildToDisk() Getting block 45 of 210 Reserving size (4338519) for bucket 45 Calculating Z arrays for bucket 45 Entering block accumulator loop for bucket 45: Returning from initFromVector bucket 28: 20% Wrote 220173300 bytes to primary EBWT file: BS_GA.rev.1.bt2 Wrote 161971392 bytes to secondary EBWT file: BS_GA.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 647885551 bwtLen: 647885552 sz: 161971388 bwtSz: 161971388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 40492847 offsSz: 161971388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3374404 numLines: 3374404 ebwtTotLen: 215961856 ebwtTotSz: 215961856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:02:26 bucket 32: 10% bucket 13: 100% Sorting block of length 2365872 for bucket 13 (Using difference cover) bucket 29: 20% bucket 31: 10% bucket 25: 100% Sorting block of length 3845088 for bucket 25 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3507836 for bucket 22 Getting block 46 of 210 Reserving size (4338519) for bucket 46 Calculating Z arrays for bucket 46 Entering block accumulator loop for bucket 46: Sorting block time: 00:00:02 Returning block of 4235339 for bucket 16 Getting block 47 of 210 Reserving size (4338519) for bucket 47 Calculating Z arrays for bucket 47 Entering block accumulator loop for bucket 47: bucket 36: 10% Sorting block time: 00:00:02 Returning block of 3987711 for bucket 27 bucket 37: 10% Getting block 48 of 210 Reserving size (4338519) for bucket 48 Calculating Z arrays for bucket 48 Entering block accumulator loop for bucket 48: Sorting block time: 00:00:01 Returning block of 2365873 for bucket 13 Sorting block time: 00:00:02 Returning block of 3087166 for bucket 23 Getting block 49 of 210 Reserving size (4338519) for bucket 49 Calculating Z arrays for bucket 49 Entering block accumulator loop for bucket 49: Getting block 50 of 210 Reserving size (4338519) for bucket 50 Calculating Z arrays for bucket 50 Entering block accumulator loop for bucket 50: bucket 20: 100% Sorting block of length 4041899 for bucket 20 (Using difference cover) bucket 39: 10% bucket 19: 100% Sorting block of length 3130968 for bucket 19 (Using difference cover) bucket 33: 10% bucket 30: 20% bucket 40: 10% bucket 28: 30% bucket 43: 10% bucket 21: 100% Sorting block of length 2533290 for bucket 21 (Using difference cover) bucket 44: 10% bucket 32: 20% Sorting block time: 00:00:02 Returning block of 3845089 for bucket 25 Getting block 51 of 210 Reserving size (4338519) for bucket 51 Calculating Z arrays for bucket 51 Entering block accumulator loop for bucket 51: bucket 29: 30% bucket 38: 10% bucket 45: 10% Sorting block time: 00:00:01 Returning block of 3130969 for bucket 19 bucket 47: 10% bucket 36: 20% Getting block 52 of 210 Reserving size (4338519) for bucket 52 Calculating Z arrays for bucket 52 Entering block accumulator loop for bucket 52: Sorting block time: 00:00:01 Returning block of 2533291 for bucket 21 Getting block 53 of 210 Reserving size (4338519) for bucket 53 Calculating Z arrays for bucket 53 Entering block accumulator loop for bucket 53: bucket 34: 10% bucket 37: 20% bucket 35: 10% Sorting block time: 00:00:02 Returning block of 4041900 for bucket 20 bucket 39: 20% Getting block 54 of 210 Reserving size (4338519) for bucket 54 Calculating Z arrays for bucket 54 Entering block accumulator loop for bucket 54: bucket 33: 20% bucket 30: 30% bucket 42: 10% bucket 41: 10% bucket 28: 40% bucket 40: 20% bucket 31: 20% bucket 43: 20% bucket 32: 30% bucket 44: 20% bucket 46: 10% bucket 29: 40% bucket 49: 10% bucket 48: 10% bucket 45: 20% bucket 50: 10% bucket 38: 20% bucket 51: 10% bucket 34: 20% bucket 36: 30% bucket 47: 20% bucket 35: 20% bucket 53: 10% bucket 52: 10% bucket 30: 40% bucket 42: 20% bucket 41: 20% bucket 37: 30% bucket 43: 30% bucket 39: 30% bucket 31: 30% bucket 28: 50% bucket 33: 30% bucket 40: 30% bucket 46: 20% bucket 54: 10% bucket 32: 40% bucket 29: 50% bucket 44: 30% bucket 49: 20% bucket 38: 30% bucket 50: 20% bucket 48: 20% bucket 34: 30% bucket 45: 30% bucket 51: 20% bucket 35: 30% bucket 30: 50% bucket 36: 40% bucket 42: 30% bucket 47: 30% bucket 43: 40% bucket 53: 20% bucket 41: 30% bucket 31: 40% bucket 52: 20% bucket 28: 60% bucket 39: 40% bucket 46: 30% bucket 37: 40% bucket 32: 50% bucket 33: 40% bucket 40: 40% bucket 38: 40% bucket 49: 30% bucket 29: 60% bucket 34: 40% bucket 44: 40% bucket 54: 20% bucket 50: 30% bucket 51: 30% bucket 35: 40% bucket 45: 40% bucket 48: 30% bucket 43: 50% bucket 42: 40% bucket 47: 40% bucket 30: 60% bucket 31: 50% bucket 41: 40% bucket 36: 50% bucket 53: 30% bucket 32: 60% bucket 28: 70% bucket 46: 40% bucket 38: 50% bucket 39: 50% bucket 33: 50% bucket 34: 50% bucket 49: 40% bucket 52: 30% bucket 40: 50% bucket 37: 50% bucket 29: 70% bucket 50: 40% bucket 44: 50% bucket 35: 50% bucket 51: 40% bucket 43: 60% bucket 54: 30% bucket 42: 50% bucket 45: 50% bucket 31: 60% bucket 47: 50% bucket 41: 50% bucket 32: 70% bucket 48: 40% bucket 30: 70% bucket 53: 40% bucket 38: 60% bucket 36: 60% bucket 46: 50% bucket 28: 80% bucket 34: 60% bucket 49: 50% bucket 39: 60% bucket 40: 60% bucket 33: 60% bucket 29: 80% bucket 35: 60% bucket 50: 50% bucket 43: 70% bucket 37: 60% bucket 52: 40% bucket 51: 50% bucket 42: 60% bucket 44: 60% bucket 31: 70% bucket 47: 60% bucket 41: 60% bucket 32: 80% bucket 45: 60% bucket 54: 40% bucket 38: 70% bucket 34: 70% bucket 30: 80% bucket 46: 60% bucket 53: 50% bucket 28: 90% bucket 49: 60% bucket 36: 70% bucket 48: 50% bucket 43: 80% bucket 35: 70% bucket 40: 70% bucket 29: 90% bucket 39: 70% bucket 33: 70% bucket 50: 60% bucket 42: 70% bucket 31: 80% bucket 51: 60% bucket 37: 70% bucket 52: 50% bucket 44: 70% bucket 32: 90% bucket 47: 70% bucket 41: 70% bucket 38: 80% bucket 45: 70% bucket 34: 80% bucket 30: 90% bucket 54: 50% bucket 46: 70% bucket 28: 100% Sorting block of length 2648331 for bucket 28 (Using difference cover) bucket 53: 60% bucket 49: 70% bucket 36: 80% bucket 48: 60% bucket 43: 90% bucket 35: 80% bucket 29: 100% Sorting block of length 4113827 for bucket 29 (Using difference cover) bucket 39: 80% bucket 40: 80% bucket 33: 80% bucket 42: 80% bucket 50: 70% bucket 31: 90% bucket 37: 80% bucket 44: 80% bucket 51: 70% bucket 32: 100% Sorting block of length 3747737 for bucket 32 (Using difference cover) bucket 52: 60% bucket 38: 90% bucket 41: 80% bucket 47: 80% bucket 34: 90% bucket 45: 80% bucket 30: 100% Sorting block of length 3009896 for bucket 30 (Using difference cover) bucket 46: 80% bucket 54: 60% bucket 36: 90% bucket 49: 80% bucket 53: 70% bucket 35: 90% bucket 43: 100% Sorting block of length 4029059 for bucket 43 (Using difference cover) bucket 48: 70% bucket 39: 90% bucket 33: 90% bucket 40: 90% Sorting block time: 00:00:01 Returning block of 2648332 for bucket 28 bucket 42: 90% Getting block 55 of 210 Reserving size (4338519) for bucket 55 Calculating Z arrays for bucket 55 Entering block accumulator loop for bucket 55: bucket 50: 80% bucket 31: 100% Sorting block of length 4010023 for bucket 31 (Using difference cover) bucket 44: 90% bucket 38: 100% Sorting block of length 1160258 for bucket 38 (Using difference cover) bucket 37: 90% bucket 34: 100% Sorting block of length 680316 for bucket 34 (Using difference cover) bucket 51: 80% bucket 47: 90% bucket 41: 90% bucket 52: 70% bucket 45: 90% Sorting block time: 00:00:01 Returning block of 3009897 for bucket 30 bucket 46: 90% Sorting block time: 00:00:00 Returning block of 680317 for bucket 34 Getting block 56 of 210 Reserving size (4338519) for bucket 56 Calculating Z arrays for bucket 56 Entering block accumulator loop for bucket 56: Sorting block time: 00:00:00 Returning block of 1160259 for bucket 38 bucket 49: 90% bucket 54: 70% bucket 36: 100% Sorting block of length 3483861 for bucket 36 (Using difference cover) Getting block 57 of 210 Reserving size (4338519) for bucket 57 Calculating Z arrays for bucket 57 Entering block accumulator loop for bucket 57: Getting block 58 of 210 Reserving size (4338519) for bucket 58 Calculating Z arrays for bucket 58 Entering block accumulator loop for bucket 58: Sorting block time: 00:00:01 Returning block of 4113828 for bucket 29 bucket 35: 100% Sorting block of length 4171216 for bucket 35 (Using difference cover) bucket 39: 100% Sorting block of length 3902527 for bucket 39 (Using difference cover) bucket 53: 80% bucket 33: 100% Sorting block of length 4131484 for bucket 33 (Using difference cover) Getting block 59 of 210 Reserving size (4338519) for bucket 59 Calculating Z arrays for bucket 59 Entering block accumulator loop for bucket 59: bucket 40: 100% Sorting block of length 3633584 for bucket 40 (Using difference cover) bucket 42: 100% Sorting block of length 2085570 for bucket 42 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3747738 for bucket 32 bucket 48: 80% Getting block 60 of 210 Reserving size (4338519) for bucket 60 Calculating Z arrays for bucket 60 Entering block accumulator loop for bucket 60: Sorting block time: 00:00:02 Returning block of 4029060 for bucket 43 bucket 50: 90% Getting block 61 of 210 Reserving size (4338519) for bucket 61 Calculating Z arrays for bucket 61 Entering block accumulator loop for bucket 61: bucket 44: 100% Sorting block of length 3063082 for bucket 44 (Using difference cover) bucket 55: 10% Sorting block time: 00:00:01 Returning block of 4010024 for bucket 31 bucket 37: 100% Sorting block of length 4216210 for bucket 37 (Using difference cover) bucket 51: 90% bucket 47: 100% Sorting block of length 3911550 for bucket 47 (Using difference cover) Getting block 62 of 210 Reserving size (4338519) for bucket 62 Calculating Z arrays for bucket 62 Entering block accumulator loop for bucket 62: bucket 41: 100% Sorting block of length 3644708 for bucket 41 (Using difference cover) bucket 45: 100% Sorting block of length 1577817 for bucket 45 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2085571 for bucket 42 Getting block 63 of 210 Reserving size (4338519) for bucket 63 Calculating Z arrays for bucket 63 Entering block accumulator loop for bucket 63: bucket 52: 80% Sorting block time: 00:00:02 Returning block of 3483862 for bucket 36 bucket 46: 100% Sorting block of length 3534122 for bucket 46 (Using difference cover) Getting block 64 of 210 Reserving size (4338519) for bucket 64 Calculating Z arrays for bucket 64 Entering block accumulator loop for bucket 64: Sorting block time: 00:00:01 Returning block of 3633585 for bucket 40 Getting block 65 of 210 Reserving size (4338519) for bucket 65 Calculating Z arrays for bucket 65 Entering block accumulator loop for bucket 65: bucket 49: 100% Sorting block of length 1020212 for bucket 49 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1577818 for bucket 45 Sorting block time: 00:00:01 Returning block of 4171217 for bucket 35 bucket 56: 10% Sorting block time: 00:00:01 Returning block of 4131485 for bucket 33 Getting block 66 of 210 Reserving size (4338519) for bucket 66 Calculating Z arrays for bucket 66 Entering block accumulator loop for bucket 66: Sorting block time: 00:00:01 Returning block of 3902528 for bucket 39 Getting block 67 of 210 Reserving size (4338519) for bucket 67 Calculating Z arrays for bucket 67 Entering block accumulator loop for bucket 67: Getting block 68 of 210 Reserving size (4338519) for bucket 68 Calculating Z arrays for bucket 68 Entering block accumulator loop for bucket 68: Getting block 69 of 210 Reserving size (4338519) for bucket 69 Calculating Z arrays for bucket 69 Entering block accumulator loop for bucket 69: bucket 57: 10% bucket 58: 10% Sorting block time: 00:00:02 Returning block of 3063083 for bucket 44 Getting block 70 of 210 Reserving size (4338519) for bucket 70 Calculating Z arrays for bucket 70 Entering block accumulator loop for bucket 70: Sorting block time: 00:00:01 Returning block of 1020213 for bucket 49 bucket 54: 80% Getting block 71 of 210 Reserving size (4338519) for bucket 71 Calculating Z arrays for bucket 71 Entering block accumulator loop for bucket 71: bucket 53: 90% bucket 59: 10% Sorting block time: 00:00:01 Returning block of 3644709 for bucket 41 Getting block 72 of 210 Reserving size (4338519) for bucket 72 Calculating Z arrays for bucket 72 Entering block accumulator loop for bucket 72: Sorting block time: 00:00:02 Returning block of 4216211 for bucket 37 Sorting block time: 00:00:01 Returning block of 3911551 for bucket 47 Getting block 73 of 210 Reserving size (4338519) for bucket 73 Calculating Z arrays for bucket 73 Entering block accumulator loop for bucket 73: bucket 48: 90% Getting block 74 of 210 Reserving size (4338519) for bucket 74 Calculating Z arrays for bucket 74 Entering block accumulator loop for bucket 74: bucket 60: 10% Sorting block time: 00:00:02 Returning block of 3534123 for bucket 46 bucket 61: 10% bucket 50: 100% Sorting block of length 3640943 for bucket 50 (Using difference cover) Getting block 75 of 210 Reserving size (4338519) for bucket 75 Calculating Z arrays for bucket 75 Entering block accumulator loop for bucket 75: bucket 55: 20% bucket 51: 100% Sorting block of length 3146508 for bucket 51 (Using difference cover) bucket 62: 10% bucket 63: 10% bucket 52: 90% bucket 64: 10% bucket 56: 20% bucket 66: 10% bucket 54: 90% Sorting block time: 00:00:01 Returning block of 3640944 for bucket 50 Getting block 76 of 210 Reserving size (4338519) for bucket 76 Calculating Z arrays for bucket 76 Entering block accumulator loop for bucket 76: bucket 71: 10% bucket 65: 10% bucket 70: 10% Sorting block time: 00:00:02 Returning block of 3146509 for bucket 51 Getting block 77 of 210 Reserving size (4338519) for bucket 77 Calculating Z arrays for bucket 77 Entering block accumulator loop for bucket 77: bucket 57: 20% bucket 73: 10% bucket 74: 10% bucket 68: 10% bucket 58: 20% bucket 67: 10% bucket 69: 10% bucket 72: 10% bucket 75: 10% bucket 60: 20% bucket 53: 100% Sorting block of length 3415778 for bucket 53 (Using difference cover) bucket 59: 20% bucket 61: 20% bucket 48: 100% Sorting block of length 3562117 for bucket 48 (Using difference cover) bucket 62: 20% bucket 63: 20% bucket 55: 30% bucket 64: 20% bucket 56: 30% bucket 76: 10% Sorting block time: 00:00:02 Returning block of 3415779 for bucket 53 bucket 54: 100% Sorting block of length 2254934 for bucket 54 (Using difference cover) bucket 52: 100% Sorting block of length 2251020 for bucket 52 (Using difference cover) Getting block 78 of 210 Reserving size (4338519) for bucket 78 Calculating Z arrays for bucket 78 Entering block accumulator loop for bucket 78: bucket 77: 10% bucket 66: 20% bucket 73: 20% bucket 74: 20% bucket 71: 20% Sorting block time: 00:00:01 Returning block of 3562118 for bucket 48 Getting block 79 of 210 Reserving size (4338519) for bucket 79 Calculating Z arrays for bucket 79 Entering block accumulator loop for bucket 79: bucket 75: 20% bucket 70: 20% bucket 60: 30% Sorting block time: 00:00:01 Returning block of 2251021 for bucket 52 bucket 57: 30% Getting block 80 of 210 Reserving size (4338519) for bucket 80 Calculating Z arrays for bucket 80 Entering block accumulator loop for bucket 80: bucket 65: 20% bucket 58: 30% Sorting block time: 00:00:01 Returning block of 2254935 for bucket 54 Getting block 81 of 210 Reserving size (4338519) for bucket 81 Calculating Z arrays for bucket 81 Entering block accumulator loop for bucket 81: bucket 72: 20% bucket 68: 20% bucket 67: 20% bucket 69: 20% bucket 59: 30% bucket 61: 30% bucket 76: 20% bucket 63: 30% bucket 56: 40% bucket 64: 30% bucket 78: 10% bucket 77: 20% bucket 73: 30% bucket 74: 30% bucket 62: 30% bucket 75: 30% bucket 66: 30% bucket 55: 40% bucket 79: 10% bucket 70: 30% bucket 81: 10% bucket 80: 10% bucket 60: 40% bucket 71: 30% bucket 72: 30% bucket 57: 40% bucket 58: 40% bucket 65: 30% bucket 76: 30% bucket 68: 30% bucket 59: 40% bucket 67: 30% bucket 77: 30% bucket 63: 40% bucket 78: 20% bucket 69: 30% bucket 74: 40% bucket 73: 40% bucket 56: 50% bucket 61: 40% bucket 75: 40% bucket 64: 40% bucket 66: 40% bucket 81: 20% bucket 80: 20% bucket 62: 40% bucket 55: 50% bucket 79: 20% bucket 70: 40% bucket 72: 40% bucket 76: 40% bucket 60: 50% bucket 71: 40% bucket 57: 50% bucket 77: 40% bucket 58: 50% bucket 78: 30% bucket 74: 50% bucket 73: 50% bucket 75: 50% bucket 56: 60% bucket 65: 40% bucket 61: 50% bucket 63: 50% bucket 64: 50% bucket 68: 40% bucket 59: 50% bucket 81: 30% bucket 67: 40% bucket 80: 30% bucket 69: 40% bucket 66: 50% bucket 76: 50% bucket 79: 30% bucket 70: 50% bucket 55: 60% bucket 62: 50% bucket 72: 50% bucket 77: 50% bucket 78: 40% bucket 74: 60% bucket 75: 60% bucket 73: 60% bucket 60: 60% bucket 57: 60% bucket 56: 70% bucket 58: 60% bucket 71: 50% bucket 61: 60% bucket 63: 60% bucket 81: 40% bucket 64: 60% bucket 65: 50% bucket 59: 60% bucket 80: 40% bucket 68: 50% bucket 67: 50% bucket 76: 60% bucket 66: 60% bucket 69: 50% bucket 79: 40% bucket 72: 60% bucket 77: 60% bucket 55: 70% bucket 75: 70% bucket 74: 70% bucket 78: 50% bucket 73: 70% bucket 70: 60% bucket 62: 60% bucket 60: 70% bucket 58: 70% bucket 56: 80% bucket 57: 70% bucket 81: 50% bucket 71: 60% bucket 61: 70% bucket 63: 70% bucket 80: 50% bucket 64: 70% bucket 59: 70% bucket 65: 60% bucket 76: 70% bucket 68: 60% bucket 79: 50% bucket 72: 70% bucket 67: 60% bucket 66: 70% bucket 69: 60% bucket 77: 70% bucket 75: 80% bucket 74: 80% bucket 78: 60% bucket 73: 80% bucket 55: 80% bucket 70: 70% bucket 62: 70% bucket 81: 60% bucket 58: 80% bucket 60: 80% bucket 56: 90% bucket 57: 80% bucket 71: 70% bucket 80: 60% bucket 61: 80% bucket 63: 80% bucket 76: 80% bucket 59: 80% bucket 64: 80% bucket 65: 70% bucket 72: 80% bucket 79: 60% bucket 75: 90% bucket 68: 70% bucket 77: 80% bucket 74: 90% bucket 78: 70% bucket 73: 90% bucket 67: 70% bucket 66: 80% bucket 69: 70% bucket 55: 90% bucket 81: 70% bucket 58: 90% bucket 56: 100% Sorting block of length 2667552 for bucket 56 (Using difference cover) bucket 70: 80% bucket 60: 90% bucket 57: 90% bucket 62: 80% bucket 80: 70% bucket 76: 90% bucket 71: 80% bucket 61: 90% bucket 63: 90% bucket 59: 90% bucket 72: 90% bucket 64: 90% bucket 79: 70% bucket 75: 100% Sorting block of length 2018174 for bucket 75 (Using difference cover) bucket 74: 100% Sorting block of length 2491442 for bucket 74 (Using difference cover) bucket 65: 80% bucket 77: 90% bucket 78: 80% bucket 73: 100% Sorting block of length 3645003 for bucket 73 (Using difference cover) bucket 68: 80% bucket 67: 80% bucket 66: 90% bucket 69: 80% bucket 55: 100% Sorting block of length 3095097 for bucket 55 (Using difference cover) bucket 81: 80% bucket 58: 100% Sorting block of length 1663390 for bucket 58 (Using difference cover) bucket 76: 100% Sorting block of length 4028547 for bucket 76 (Using difference cover) bucket 80: 80% bucket 57: 100% Sorting block of length 3882851 for bucket 57 (Using difference cover) bucket 60: 100% Sorting block of length 2396535 for bucket 60 (Using difference cover) bucket 62: 90% bucket 70: 90% bucket 72: 100% Sorting block of length 3627012 for bucket 72 (Using difference cover) bucket 71: 90% bucket 61: 100% Sorting block of length 3999786 for bucket 61 (Using difference cover) bucket 79: 80% bucket 63: 100% Sorting block of length 1972337 for bucket 63 (Using difference cover) bucket 59: 100% Sorting block of length 2682755 for bucket 59 (Using difference cover) bucket 77: 100% Sorting block of length 3860708 for bucket 77 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2667553 for bucket 56 bucket 78: 90% bucket 64: 100% Sorting block of length 3841024 for bucket 64 (Using difference cover) Getting block 82 of 210 Reserving size (4338519) for bucket 82 Calculating Z arrays for bucket 82 Entering block accumulator loop for bucket 82: bucket 65: 90% Sorting block time: 00:00:01 Returning block of 2018175 for bucket 75 Getting block 83 of 210 Reserving size (4338519) for bucket 83 Calculating Z arrays for bucket 83 Entering block accumulator loop for bucket 83: bucket 68: 90% bucket 67: 90% Sorting block time: 00:00:01 Returning block of 2491443 for bucket 74 bucket 66: 100% Sorting block of length 3004302 for bucket 66 (Using difference cover) bucket 69: 90% bucket 81: 90% Getting block 84 of 210 Reserving size (4338519) for bucket 84 Calculating Z arrays for bucket 84 Entering block accumulator loop for bucket 84: Sorting block time: 00:00:00 Returning block of 1663391 for bucket 58 bucket 80: 90% Getting block 85 of 210 Reserving size (4338519) for bucket 85 Calculating Z arrays for bucket 85 Entering block accumulator loop for bucket 85: bucket 79: 90% bucket 62: 100% Sorting block of length 3642312 for bucket 62 (Using difference cover) bucket 71: 100% Sorting block of length 4058247 for bucket 71 (Using difference cover) bucket 70: 100% Sorting block of length 3486440 for bucket 70 (Using difference cover) bucket 78: 100% Sorting block of length 4117202 for bucket 78 (Using difference cover) bucket 82: 10% Sorting block time: 00:00:02 Returning block of 3645004 for bucket 73 Sorting block time: 00:00:01 Returning block of 2396536 for bucket 60 bucket 83: 10% Getting block 86 of 210 Reserving size (4338519) for bucket 86 Calculating Z arrays for bucket 86 Entering block accumulator loop for bucket 86: Sorting block time: 00:00:01 Returning block of 1972338 for bucket 63 Sorting block time: 00:00:01 Returning block of 3095098 for bucket 55 Getting block 87 of 210 Reserving size (4338519) for bucket 87 Calculating Z arrays for bucket 87 Entering block accumulator loop for bucket 87: Getting block 88 of 210 Reserving size (4338519) for bucket 88 Calculating Z arrays for bucket 88 Entering block accumulator loop for bucket 88: bucket 65: 100% Sorting block of length 661846 for bucket 65 (Using difference cover) Getting block 89 of 210 Reserving size (4338519) for bucket 89 Calculating Z arrays for bucket 89 Entering block accumulator loop for bucket 89: Sorting block time: 00:00:01 Returning block of 2682756 for bucket 59 Getting block 90 of 210 Reserving size (4338519) for bucket 90 Calculating Z arrays for bucket 90 Entering block accumulator loop for bucket 90: Sorting block time: 00:00:00 Returning block of 661847 for bucket 65 Getting block 91 of 210 Reserving size (4338519) for bucket 91 Calculating Z arrays for bucket 91 Entering block accumulator loop for bucket 91: Sorting block time: 00:00:01 Returning block of 3882852 for bucket 57 Getting block 92 of 210 Reserving size (4338519) for bucket 92 Calculating Z arrays for bucket 92 Entering block accumulator loop for bucket 92: Sorting block time: 00:00:01 Returning block of 4028548 for bucket 76 Sorting block time: 00:00:02 Returning block of 3627013 for bucket 72 bucket 81: 100% Sorting block of length 4287424 for bucket 81 (Using difference cover) bucket 84: 10% bucket 68: 100% Sorting block of length 3566568 for bucket 68 (Using difference cover) Getting block 93 of 210 Reserving size (4338519) for bucket 93 Getting block 94 of 210 Calculating Z arrays for bucket 93 Reserving size (4338519) for bucket 94 Calculating Z arrays for bucket 94 Entering block accumulator loop for bucket 93: Entering block accumulator loop for bucket 94: bucket 85: 10% bucket 80: 100% Sorting block of length 3110119 for bucket 80 (Using difference cover) bucket 67: 100% Sorting block of length 2311115 for bucket 67 (Using difference cover) bucket 69: 100% Sorting block of length 1409997 for bucket 69 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3841025 for bucket 64 Sorting block time: 00:00:02 Returning block of 3004303 for bucket 66 Getting block 95 of 210 Reserving size (4338519) for bucket 95 Calculating Z arrays for bucket 95 Entering block accumulator loop for bucket 95: Getting block 96 of 210 Reserving size (4338519) for bucket 96 Calculating Z arrays for bucket 96 Entering block accumulator loop for bucket 96: Sorting block time: 00:00:02 Returning block of 3999787 for bucket 61 Sorting block time: 00:00:02 Returning block of 3860709 for bucket 77 Getting block 97 of 210 Reserving size (4338519) for bucket 97 Calculating Z arrays for bucket 97 Entering block accumulator loop for bucket 97: Getting block 98 of 210 Reserving size (4338519) for bucket 98 Calculating Z arrays for bucket 98 Entering block accumulator loop for bucket 98: bucket 79: 100% Sorting block of length 3309990 for bucket 79 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3486441 for bucket 70 Sorting block time: 00:00:00 Returning block of 1409998 for bucket 69 bucket 83: 20% Getting block 99 of 210 Reserving size (4338519) for bucket 99 Calculating Z arrays for bucket 99 Entering block accumulator loop for bucket 99: Sorting block time: 00:00:01 Returning block of 3642313 for bucket 62 Getting block 100 of 210 Reserving size (4338519) for bucket 100 Calculating Z arrays for bucket 100 Entering block accumulator loop for bucket 100: bucket 82: 20% Getting block 101 of 210 Reserving size (4338519) for bucket 101 Calculating Z arrays for bucket 101 Entering block accumulator loop for bucket 101: Sorting block time: 00:00:02 Returning block of 4117203 for bucket 78 Getting block 102 of 210 Reserving size (4338519) for bucket 102 Calculating Z arrays for bucket 102 Entering block accumulator loop for bucket 102: Sorting block time: 00:00:01 Returning block of 2311116 for bucket 67 bucket 88: 10% Sorting block time: 00:00:02 Returning block of 4058248 for bucket 71 Getting block 103 of 210 Reserving size (4338519) for bucket 103 Calculating Z arrays for bucket 103 Entering block accumulator loop for bucket 103: bucket 86: 10% bucket 89: 10% bucket 87: 10% Getting block 104 of 210 Reserving size (4338519) for bucket 104 Calculating Z arrays for bucket 104 Entering block accumulator loop for bucket 104: Sorting block time: 00:00:01 Returning block of 3110120 for bucket 80 Getting block 105 of 210 Reserving size (4338519) for bucket 105 Calculating Z arrays for bucket 105 Entering block accumulator loop for bucket 105: bucket 85: 20% bucket 94: 10% Sorting block time: 00:00:01 Returning block of 3566569 for bucket 68 Sorting block time: 00:00:01 Returning block of 4287425 for bucket 81 bucket 93: 10% bucket 90: 10% bucket 84: 20% Getting block 106 of 210 Reserving size (4338519) for bucket 106 Calculating Z arrays for bucket 106 Entering block accumulator loop for bucket 106: Getting block 107 of 210 Reserving size (4338519) for bucket 107 Calculating Z arrays for bucket 107 Entering block accumulator loop for bucket 107: Sorting block time: 00:00:02 Returning block of 3309991 for bucket 79 Getting block 108 of 210 Reserving size (4338519) for bucket 108 Calculating Z arrays for bucket 108 Entering block accumulator loop for bucket 108: bucket 92: 10% bucket 91: 10% bucket 95: 10% bucket 96: 10% bucket 97: 10% bucket 98: 10% bucket 83: 30% bucket 88: 20% bucket 82: 30% bucket 102: 10% bucket 99: 10% bucket 89: 20% bucket 100: 10% bucket 101: 10% bucket 86: 20% bucket 84: 30% bucket 87: 20% bucket 93: 20% bucket 104: 10% bucket 94: 20% bucket 85: 30% bucket 103: 10% bucket 95: 20% bucket 105: 10% bucket 90: 20% bucket 106: 10% bucket 83: 40% bucket 96: 20% bucket 97: 20% bucket 98: 20% bucket 92: 20% bucket 108: 10% bucket 91: 20% bucket 107: 10% bucket 88: 30% bucket 82: 40% bucket 102: 20% bucket 89: 30% bucket 84: 40% bucket 101: 20% bucket 99: 20% bucket 86: 30% bucket 93: 30% bucket 100: 20% bucket 104: 20% bucket 87: 30% bucket 95: 30% bucket 94: 30% bucket 83: 50% bucket 103: 20% bucket 85: 40% bucket 97: 30% bucket 98: 30% bucket 96: 30% bucket 90: 30% bucket 105: 20% bucket 88: 40% bucket 92: 30% bucket 106: 20% bucket 91: 30% bucket 107: 20% bucket 108: 20% bucket 84: 50% bucket 102: 30% bucket 82: 50% bucket 101: 30% bucket 89: 40% bucket 83: 60% bucket 93: 40% bucket 95: 40% bucket 104: 30% bucket 94: 40% bucket 86: 40% bucket 99: 30% bucket 103: 30% bucket 85: 50% bucket 98: 40% bucket 97: 40% bucket 87: 40% bucket 96: 40% bucket 100: 30% bucket 88: 50% bucket 90: 40% bucket 105: 30% bucket 84: 60% bucket 92: 40% bucket 91: 40% bucket 83: 70% bucket 82: 60% bucket 102: 40% bucket 106: 30% bucket 93: 50% bucket 101: 40% bucket 107: 30% bucket 108: 30% bucket 95: 50% bucket 94: 50% bucket 104: 40% bucket 89: 50% bucket 86: 50% bucket 103: 40% bucket 97: 50% bucket 98: 50% bucket 96: 50% bucket 85: 60% bucket 99: 40% bucket 88: 60% bucket 87: 50% bucket 100: 40% bucket 84: 70% bucket 90: 50% bucket 83: 80% bucket 105: 40% bucket 102: 50% bucket 93: 60% bucket 82: 70% bucket 92: 50% bucket 101: 50% bucket 95: 60% bucket 91: 50% bucket 94: 60% bucket 104: 50% bucket 106: 40% bucket 97: 60% bucket 98: 60% bucket 107: 40% bucket 88: 70% bucket 96: 60% bucket 103: 50% bucket 89: 60% bucket 108: 40% bucket 86: 60% bucket 85: 70% bucket 84: 80% bucket 99: 50% bucket 83: 90% bucket 87: 60% bucket 100: 50% bucket 90: 60% bucket 93: 70% bucket 82: 80% bucket 102: 60% bucket 95: 70% bucket 105: 50% bucket 94: 70% bucket 101: 60% bucket 92: 60% bucket 91: 60% bucket 104: 60% bucket 88: 80% bucket 98: 70% bucket 97: 70% bucket 89: 70% bucket 86: 70% bucket 96: 70% bucket 85: 80% bucket 84: 90% bucket 103: 60% bucket 106: 50% bucket 107: 50% bucket 83: 100% Sorting block of length 1488231 for bucket 83 (Using difference cover) bucket 108: 50% bucket 99: 60% bucket 87: 70% bucket 90: 70% bucket 100: 60% bucket 82: 90% bucket 93: 80% bucket 95: 80% bucket 94: 80% bucket 102: 70% bucket 92: 70% bucket 101: 70% bucket 91: 70% bucket 88: 90% bucket 104: 70% bucket 85: 90% bucket 84: 100% Sorting block of length 4200341 for bucket 84 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1488232 for bucket 83 bucket 98: 80% bucket 97: 80% bucket 105: 60% bucket 89: 80% Getting block 109 of 210 Reserving size (4338519) for bucket 109 Calculating Z arrays for bucket 109 Entering block accumulator loop for bucket 109: bucket 96: 80% bucket 86: 80% bucket 103: 70% bucket 106: 60% bucket 107: 60% bucket 87: 80% bucket 99: 70% bucket 108: 60% bucket 90: 80% bucket 82: 100% Sorting block of length 3755559 for bucket 82 (Using difference cover) bucket 100: 70% bucket 95: 90% bucket 93: 90% bucket 94: 90% bucket 92: 80% bucket 85: 100% Sorting block of length 2265606 for bucket 85 (Using difference cover) bucket 102: 80% bucket 91: 80% bucket 101: 80% bucket 88: 100% Sorting block of length 1749825 for bucket 88 (Using difference cover) bucket 104: 80% bucket 98: 90% bucket 89: 90% bucket 97: 90% bucket 96: 90% bucket 109: 10% bucket 86: 90% bucket 103: 80% bucket 105: 70% bucket 87: 90% bucket 99: 80% bucket 90: 90% bucket 106: 70% bucket 107: 70% bucket 108: 70% bucket 100: 80% bucket 95: 100% Sorting block of length 2568364 for bucket 95 (Using difference cover) bucket 93: 100% Sorting block of length 3644373 for bucket 93 (Using difference cover) bucket 94: 100% Sorting block of length 3769772 for bucket 94 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1749826 for bucket 88 Getting block 110 of 210 Reserving size (4338519) for bucket 110 Calculating Z arrays for bucket 110 Entering block accumulator loop for bucket 110: bucket 92: 90% bucket 91: 90% bucket 102: 90% bucket 101: 90% Sorting block time: 00:00:01 Returning block of 2265607 for bucket 85 bucket 89: 100% Sorting block of length 3836013 for bucket 89 (Using difference cover) bucket 98: 100% Sorting block of length 2574067 for bucket 98 (Using difference cover) bucket 97: 100% Sorting block of length 4149516 for bucket 97 (Using difference cover) Getting block 111 of 210 Reserving size (4338519) for bucket 111 Calculating Z arrays for bucket 111 Entering block accumulator loop for bucket 111: bucket 104: 90% Sorting block time: 00:00:02 Returning block of 4200342 for bucket 84 bucket 96: 100% Sorting block of length 3319862 for bucket 96 (Using difference cover) bucket 87: 100% Sorting block of length 3526290 for bucket 87 (Using difference cover) Getting block 112 of 210 Reserving size (4338519) for bucket 112 Calculating Z arrays for bucket 112 Entering block accumulator loop for bucket 112: bucket 86: 100% Sorting block of length 4081923 for bucket 86 (Using difference cover) bucket 90: 100% Sorting block of length 1750560 for bucket 90 (Using difference cover) bucket 103: 90% bucket 99: 90% bucket 109: 20% Sorting block time: 00:00:02 Returning block of 3755560 for bucket 82 bucket 106: 80% Getting block 113 of 210 Reserving size (4338519) for bucket 113 Calculating Z arrays for bucket 113 Entering block accumulator loop for bucket 113: bucket 107: 80% bucket 105: 80% bucket 108: 80% bucket 100: 90% Sorting block time: 00:00:01 Returning block of 2568365 for bucket 95 Sorting block time: 00:00:00 Returning block of 1750561 for bucket 90 Getting block 114 of 210 Reserving size (4338519) for bucket 114 Calculating Z arrays for bucket 114 Entering block accumulator loop for bucket 114: Getting block 115 of 210 Reserving size (4338519) for bucket 115 Calculating Z arrays for bucket 115 Entering block accumulator loop for bucket 115: Sorting block time: 00:00:01 Returning block of 2574068 for bucket 98 Getting block 116 of 210 Reserving size (4338519) for bucket 116 Calculating Z arrays for bucket 116 Entering block accumulator loop for bucket 116: bucket 110: 10% bucket 92: 100% Sorting block of length 3654533 for bucket 92 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3644374 for bucket 93 bucket 91: 100% Sorting block of length 4076545 for bucket 91 (Using difference cover) bucket 102: 100% Sorting block of length 3876004 for bucket 102 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3769773 for bucket 94 Getting block 117 of 210 Reserving size (4338519) for bucket 117 Calculating Z arrays for bucket 117 Entering block accumulator loop for bucket 117: Sorting block time: 00:00:01 Returning block of 3836014 for bucket 89 Getting block 118 of 210 Reserving size (4338519) for bucket 118 Calculating Z arrays for bucket 118 Entering block accumulator loop for bucket 118: bucket 104: 100% Sorting block of length 2358975 for bucket 104 (Using difference cover) Getting block 119 of 210 Reserving size (4338519) for bucket 119 Calculating Z arrays for bucket 119 Entering block accumulator loop for bucket 119: Sorting block time: 00:00:01 Returning block of 3319863 for bucket 96 Getting block 120 of 210 Reserving size (4338519) for bucket 120 Calculating Z arrays for bucket 120 Entering block accumulator loop for bucket 120: Sorting block time: 00:00:01 Returning block of 3526291 for bucket 87 Getting block 121 of 210 Reserving size (4338519) for bucket 121 Calculating Z arrays for bucket 121 Entering block accumulator loop for bucket 121: bucket 101: 100% Sorting block of length 4010430 for bucket 101 (Using difference cover) Sorting block time: 00:00:01 Returning block of 4149517 for bucket 97 Getting block 122 of 210 Reserving size (4338519) for bucket 122 Calculating Z arrays for bucket 122 Entering block accumulator loop for bucket 122: Sorting block time: 00:00:02 Returning block of 4081924 for bucket 86 Getting block 123 of 210 Reserving size (4338519) for bucket 123 Calculating Z arrays for bucket 123 Entering block accumulator loop for bucket 123: bucket 112: 10% bucket 111: 10% bucket 103: 100% Sorting block of length 2033315 for bucket 103 (Using difference cover) bucket 99: 100% Sorting block of length 2150060 for bucket 99 (Using difference cover) bucket 109: 30% Sorting block time: 00:00:01 Returning block of 2358976 for bucket 104 Getting block 124 of 210 Reserving size (4338519) for bucket 124 Calculating Z arrays for bucket 124 Entering block accumulator loop for bucket 124: bucket 107: 90% Sorting block time: 00:00:01 Returning block of 3654534 for bucket 92 bucket 106: 90% Getting block 125 of 210 Reserving size (4338519) for bucket 125 Calculating Z arrays for bucket 125 Entering block accumulator loop for bucket 125: Sorting block time: 00:00:02 Returning block of 4076546 for bucket 91 Sorting block time: 00:00:01 Returning block of 2033316 for bucket 103 bucket 100: 100% Sorting block of length 3025813 for bucket 100 (Using difference cover) Getting block 126 of 210 Reserving size (4338519) for bucket 126 Calculating Z arrays for bucket 126 Entering block accumulator loop for bucket 126: Getting block 127 of 210 Reserving size (4338519) for bucket 127 Calculating Z arrays for bucket 127 Entering block accumulator loop for bucket 127: bucket 108: 90% Sorting block time: 00:00:02 Returning block of 3876005 for bucket 102 Sorting block time: 00:00:01 Returning block of 2150061 for bucket 99 bucket 113: 10% Getting block 128 of 210 Reserving size (4338519) for bucket 128 Calculating Z arrays for bucket 128 Entering block accumulator loop for bucket 128: Getting block 129 of 210 Reserving size (4338519) for bucket 129 Calculating Z arrays for bucket 129 Entering block accumulator loop for bucket 129: bucket 105: 90% bucket 115: 10% Sorting block time: 00:00:02 Returning block of 4010431 for bucket 101 Getting block 130 of 210 Reserving size (4338519) for bucket 130 Calculating Z arrays for bucket 130 Entering block accumulator loop for bucket 130: bucket 110: 20% bucket 119: 10% bucket 121: 10% bucket 123: 10% bucket 111: 20% Sorting block time: 00:00:01 Returning block of 3025814 for bucket 100 Getting block 131 of 210 Reserving size (4338519) for bucket 131 Calculating Z arrays for bucket 131 Entering block accumulator loop for bucket 131: bucket 114: 10% bucket 107: 100% Sorting block of length 1786291 for bucket 107 (Using difference cover) bucket 116: 10% bucket 106: 100% Sorting block of length 3136826 for bucket 106 (Using difference cover) bucket 125: 10% bucket 108: 100% Sorting block of length 3792934 for bucket 108 (Using difference cover) bucket 127: 10% bucket 117: 10% bucket 118: 10% bucket 129: 10% bucket 115: 20% bucket 130: 10% Sorting block time: 00:00:00 Returning block of 1786292 for bucket 107 Getting block 132 of 210 Reserving size (4338519) for bucket 132 Calculating Z arrays for bucket 132 Entering block accumulator loop for bucket 132: bucket 120: 10% bucket 122: 10% bucket 119: 20% bucket 121: 20% bucket 123: 20% Sorting block time: 00:00:01 Returning block of 3136827 for bucket 106 bucket 111: 30% Getting block 133 of 210 Reserving size (4338519) for bucket 133 Calculating Z arrays for bucket 133 Entering block accumulator loop for bucket 133: bucket 114: 20% bucket 112: 20% bucket 131: 10% bucket 124: 10% Sorting block time: 00:00:01 Returning block of 3792935 for bucket 108 Getting block 134 of 210 Reserving size (4338519) for bucket 134 Calculating Z arrays for bucket 134 Entering block accumulator loop for bucket 134: bucket 109: 40% bucket 110: 30% bucket 125: 20% bucket 127: 20% bucket 126: 10% bucket 113: 20% bucket 128: 10% bucket 129: 20% bucket 115: 30% bucket 130: 20% bucket 132: 10% bucket 105: 100% Sorting block of length 3799129 for bucket 105 (Using difference cover) bucket 119: 30% bucket 123: 30% bucket 121: 30% bucket 111: 40% bucket 122: 20% bucket 114: 30% bucket 131: 20% bucket 116: 20% bucket 125: 30% bucket 134: 10% bucket 127: 30% bucket 120: 20% bucket 117: 20% Sorting block time: 00:00:02 Returning block of 3799130 for bucket 105 Getting block 135 of 210 Reserving size (4338519) for bucket 135 Calculating Z arrays for bucket 135 Entering block accumulator loop for bucket 135: bucket 118: 20% bucket 124: 20% bucket 129: 30% bucket 115: 40% bucket 130: 30% bucket 132: 20% bucket 123: 40% bucket 119: 40% bucket 133: 10% bucket 121: 40% bucket 111: 50% bucket 112: 30% bucket 114: 40% bucket 131: 30% bucket 125: 40% bucket 134: 20% bucket 109: 50% bucket 110: 40% bucket 127: 40% bucket 126: 20% bucket 120: 30% bucket 128: 20% bucket 113: 30% bucket 115: 50% bucket 129: 40% bucket 130: 40% bucket 132: 30% bucket 122: 30% bucket 123: 50% bucket 119: 50% bucket 111: 60% bucket 121: 50% bucket 114: 50% bucket 131: 40% bucket 125: 50% bucket 134: 30% bucket 127: 50% bucket 116: 30% bucket 120: 40% bucket 124: 30% bucket 115: 60% bucket 129: 50% bucket 117: 30% bucket 132: 40% bucket 130: 50% bucket 118: 30% bucket 123: 60% bucket 135: 10% bucket 119: 60% bucket 111: 70% bucket 121: 60% bucket 114: 60% bucket 112: 40% bucket 131: 50% bucket 133: 20% bucket 125: 60% bucket 134: 40% bucket 127: 60% bucket 109: 60% bucket 120: 50% bucket 110: 50% bucket 126: 30% bucket 115: 70% bucket 128: 30% bucket 129: 60% bucket 132: 50% bucket 130: 60% bucket 113: 40% bucket 123: 70% bucket 119: 70% bucket 111: 80% bucket 121: 70% bucket 122: 40% bucket 114: 70% bucket 131: 60% bucket 125: 70% bucket 127: 70% bucket 134: 50% bucket 120: 60% bucket 115: 80% bucket 124: 40% bucket 116: 40% bucket 129: 70% bucket 132: 60% bucket 117: 40% bucket 130: 70% bucket 123: 80% bucket 111: 90% bucket 119: 80% bucket 121: 80% bucket 118: 40% bucket 114: 80% bucket 135: 20% bucket 131: 70% bucket 125: 80% bucket 112: 50% bucket 127: 80% bucket 134: 60% bucket 133: 30% bucket 120: 70% bucket 109: 70% bucket 115: 90% bucket 132: 70% bucket 123: 90% bucket 129: 80% bucket 111: 100% Sorting block of length 3159459 for bucket 111 (Using difference cover) bucket 130: 80% bucket 110: 60% bucket 126: 40% bucket 119: 90% bucket 128: 40% bucket 121: 90% bucket 113: 50% bucket 114: 90% bucket 122: 50% bucket 125: 90% bucket 131: 80% bucket 127: 90% Sorting block time: 00:00:01 Returning block of 3159460 for bucket 111 Getting block 136 of 210 Reserving size (4338519) for bucket 136 Calculating Z arrays for bucket 136 Entering block accumulator loop for bucket 136: bucket 134: 70% bucket 120: 80% bucket 115: 100% Sorting block of length 4102603 for bucket 115 (Using difference cover) bucket 124: 50% bucket 123: 100% Sorting block of length 4125033 for bucket 123 (Using difference cover) bucket 132: 80% bucket 119: 100% Sorting block of length 3956266 for bucket 119 (Using difference cover) bucket 130: 90% bucket 129: 90% bucket 121: 100% Sorting block of length 3198757 for bucket 121 (Using difference cover) bucket 114: 100% Sorting block of length 3815958 for bucket 114 (Using difference cover) bucket 117: 50% bucket 116: 50% bucket 118: 50% bucket 125: 100% Sorting block of length 3639037 for bucket 125 (Using difference cover) bucket 113: 60% bucket 131: 90% bucket 127: 100% Sorting block of length 3423504 for bucket 127 (Using difference cover) bucket 135: 30% bucket 112: 60% bucket 134: 80% bucket 120: 90% Sorting block time: 00:00:02 Returning block of 4102604 for bucket 115 Getting block 137 of 210 Reserving size (4338519) for bucket 137 Calculating Z arrays for bucket 137 Entering block accumulator loop for bucket 137: Sorting block time: 00:00:02 Returning block of 4125034 for bucket 123 Sorting block time: 00:00:02 Returning block of 3198758 for bucket 121 Sorting block time: 00:00:02 Returning block of 3956267 for bucket 119 Getting block 138 of 210 Reserving size (4338519) for bucket 138 Calculating Z arrays for bucket 138 Entering block accumulator loop for bucket 138: Getting block 139 of 210 Reserving size (4338519) for bucket 139 Calculating Z arrays for bucket 139 Entering block accumulator loop for bucket 139: Getting block 140 of 210 Reserving size (4338519) for bucket 140 Calculating Z arrays for bucket 140 Entering block accumulator loop for bucket 140: bucket 132: 90% bucket 130: 100% Sorting block of length 2125879 for bucket 130 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3815959 for bucket 114 bucket 129: 100% Sorting block of length 4067446 for bucket 129 (Using difference cover) bucket 133: 40% Getting block 141 of 210 Reserving size (4338519) for bucket 141 Calculating Z arrays for bucket 141 Entering block accumulator loop for bucket 141: bucket 109: 80% Sorting block time: 00:00:01 Returning block of 3639038 for bucket 125 Getting block 142 of 210 Reserving size (4338519) for bucket 142 Calculating Z arrays for bucket 142 Entering block accumulator loop for bucket 142: bucket 128: 50% bucket 126: 50% bucket 110: 70% Sorting block time: 00:00:02 Returning block of 3423505 for bucket 127 Getting block 143 of 210 Reserving size (4338519) for bucket 143 Calculating Z arrays for bucket 143 Entering block accumulator loop for bucket 143: bucket 113: 70% bucket 131: 100% Sorting block of length 3828561 for bucket 131 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2125880 for bucket 130 bucket 122: 60% Getting block 144 of 210 Reserving size (4338519) for bucket 144 Calculating Z arrays for bucket 144 Entering block accumulator loop for bucket 144: bucket 134: 90% bucket 120: 100% Sorting block of length 4304481 for bucket 120 (Using difference cover) bucket 138: 10% bucket 139: 10% bucket 137: 10% bucket 140: 10% Sorting block time: 00:00:02 Returning block of 4067447 for bucket 129 bucket 136: 10% Getting block 145 of 210 Reserving size (4338519) for bucket 145 Calculating Z arrays for bucket 145 Entering block accumulator loop for bucket 145: bucket 132: 100% Sorting block of length 1879174 for bucket 132 (Using difference cover) bucket 141: 10% bucket 124: 60% Sorting block time: 00:00:02 Returning block of 3828562 for bucket 131 bucket 142: 10% Getting block 146 of 210 Reserving size (4338519) for bucket 146 Calculating Z arrays for bucket 146 Entering block accumulator loop for bucket 146: bucket 143: 10% bucket 113: 80% Sorting block time: 00:00:01 Returning block of 1879175 for bucket 132 Getting block 147 of 210 Reserving size (4338519) for bucket 147 Calculating Z arrays for bucket 147 Entering block accumulator loop for bucket 147: bucket 117: 60% bucket 116: 60% bucket 144: 10% Sorting block time: 00:00:02 Returning block of 4304482 for bucket 120 bucket 118: 60% Getting block 148 of 210 Reserving size (4338519) for bucket 148 Calculating Z arrays for bucket 148 Entering block accumulator loop for bucket 148: bucket 134: 100% Sorting block of length 2893071 for bucket 134 (Using difference cover) bucket 112: 70% bucket 135: 40% bucket 138: 20% bucket 139: 20% bucket 140: 20% bucket 137: 20% bucket 145: 10% bucket 141: 20% bucket 142: 20% bucket 146: 10% Sorting block time: 00:00:01 Returning block of 2893072 for bucket 134 Getting block 149 of 210 Reserving size (4338519) for bucket 149 Calculating Z arrays for bucket 149 Entering block accumulator loop for bucket 149: bucket 133: 50% bucket 143: 20% bucket 109: 90% bucket 113: 90% bucket 147: 10% bucket 128: 60% bucket 126: 60% bucket 110: 80% bucket 144: 20% bucket 122: 70% bucket 148: 10% bucket 138: 30% bucket 139: 30% bucket 140: 30% bucket 137: 30% bucket 145: 20% bucket 141: 30% bucket 124: 70% bucket 142: 30% bucket 146: 20% bucket 149: 10% bucket 136: 20% bucket 143: 30% bucket 113: 100% Sorting block of length 4053380 for bucket 113 (Using difference cover) bucket 147: 20% bucket 117: 70% bucket 144: 30% bucket 148: 20% bucket 116: 70% bucket 118: 70% bucket 112: 80% bucket 138: 40% bucket 139: 40% bucket 140: 40% bucket 145: 30% bucket 137: 40% bucket 141: 40% Sorting block time: 00:00:01 Returning block of 4053381 for bucket 113 Getting block 150 of 210 Reserving size (4338519) for bucket 150 Calculating Z arrays for bucket 150 Entering block accumulator loop for bucket 150: bucket 135: 50% bucket 142: 40% bucket 149: 20% bucket 146: 30% bucket 143: 40% bucket 109: 100% Sorting block of length 2922177 for bucket 109 (Using difference cover) bucket 133: 60% bucket 128: 70% bucket 147: 30% bucket 126: 70% bucket 110: 90% bucket 122: 80% bucket 144: 40% bucket 124: 80% bucket 148: 30% bucket 138: 50% bucket 139: 50% bucket 136: 30% bucket 140: 50% bucket 117: 80% bucket 145: 40% bucket 118: 80% bucket 141: 50% bucket 116: 80% bucket 137: 50% bucket 112: 90% bucket 150: 10% bucket 142: 50% bucket 135: 60% bucket 149: 30% bucket 146: 40% bucket 143: 50% bucket 128: 80% bucket 133: 70% bucket 147: 40% bucket 126: 80% bucket 122: 90% bucket 110: 100% Sorting block of length 4166333 for bucket 110 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2922178 for bucket 109 bucket 124: 90% bucket 144: 50% Getting block 151 of 210 Reserving size (4338519) for bucket 151 Calculating Z arrays for bucket 151 Entering block accumulator loop for bucket 151: bucket 148: 40% bucket 138: 60% bucket 139: 60% bucket 140: 60% bucket 145: 50% bucket 141: 60% bucket 137: 60% bucket 117: 90% bucket 150: 20% bucket 142: 60% bucket 136: 40% bucket 149: 40% bucket 143: 60% bucket 112: 100% Sorting block of length 1606658 for bucket 112 (Using difference cover) bucket 146: 50% bucket 118: 90% bucket 116: 90% bucket 126: 90% bucket 135: 70% Sorting block time: 00:00:02 Returning block of 4166334 for bucket 110 bucket 128: 90% Getting block 152 of 210 Reserving size (4338519) for bucket 152 Calculating Z arrays for bucket 152 Entering block accumulator loop for bucket 152: bucket 144: 60% bucket 133: 80% bucket 147: 50% bucket 151: 10% bucket 122: 100% Sorting block of length 3418444 for bucket 122 (Using difference cover) bucket 139: 70% bucket 138: 70% Sorting block time: 00:00:01 Returning block of 1606659 for bucket 112 Getting block 153 of 210 Reserving size (4338519) for bucket 153 Calculating Z arrays for bucket 153 Entering block accumulator loop for bucket 153: bucket 140: 70% bucket 145: 60% bucket 124: 100% Sorting block of length 1654665 for bucket 124 (Using difference cover) bucket 141: 70% bucket 142: 70% bucket 150: 30% bucket 137: 70% bucket 117: 100% Sorting block of length 3391033 for bucket 117 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1654666 for bucket 124 Getting block 154 of 210 Reserving size (4338519) for bucket 154 Calculating Z arrays for bucket 154 Entering block accumulator loop for bucket 154: bucket 149: 50% bucket 143: 70% Sorting block time: 00:00:01 Returning block of 3418445 for bucket 122 Getting block 155 of 210 Reserving size (4338519) for bucket 155 Calculating Z arrays for bucket 155 Entering block accumulator loop for bucket 155: bucket 146: 60% bucket 126: 100% Sorting block of length 3322128 for bucket 126 (Using difference cover) bucket 148: 50% bucket 144: 70% Sorting block time: 00:00:02 Returning block of 3391034 for bucket 117 bucket 139: 80% Getting block 156 of 210 Reserving size (4338519) for bucket 156 Calculating Z arrays for bucket 156 Entering block accumulator loop for bucket 156: bucket 138: 80% bucket 140: 80% bucket 136: 50% bucket 145: 70% bucket 118: 100% Sorting block of length 2450307 for bucket 118 (Using difference cover) bucket 116: 100% Sorting block of length 2375741 for bucket 116 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3322129 for bucket 126 bucket 141: 80% Getting block 157 of 210 Reserving size (4338519) for bucket 157 Calculating Z arrays for bucket 157 Entering block accumulator loop for bucket 157: bucket 142: 80% bucket 150: 40% bucket 135: 80% bucket 128: 100% Sorting block of length 1673166 for bucket 128 (Using difference cover) bucket 137: 80% bucket 152: 10% Sorting block time: 00:00:01 Returning block of 2450308 for bucket 118 bucket 143: 80% bucket 149: 60% bucket 133: 90% bucket 147: 60% Getting block 158 of 210 Reserving size (4338519) for bucket 158 Calculating Z arrays for bucket 158 Entering block accumulator loop for bucket 158: Sorting block time: 00:00:01 Returning block of 2375742 for bucket 116 bucket 151: 20% Getting block 159 of 210 Reserving size (4338519) for bucket 159 Calculating Z arrays for bucket 159 Entering block accumulator loop for bucket 159: bucket 146: 70% bucket 153: 10% bucket 154: 10% Sorting block time: 00:00:00 Returning block of 1673167 for bucket 128 Getting block 160 of 210 Reserving size (4338519) for bucket 160 Calculating Z arrays for bucket 160 Entering block accumulator loop for bucket 160: bucket 155: 10% bucket 148: 60% bucket 144: 80% bucket 136: 60% bucket 156: 10% bucket 139: 90% bucket 138: 90% bucket 140: 90% bucket 157: 10% bucket 145: 80% bucket 135: 90% bucket 141: 90% bucket 158: 10% bucket 152: 20% bucket 147: 70% bucket 133: 100% Sorting block of length 3389520 for bucket 133 (Using difference cover) bucket 142: 90% bucket 151: 30% bucket 159: 10% bucket 150: 50% bucket 154: 20% bucket 160: 10% bucket 143: 90% bucket 137: 90% bucket 149: 70% bucket 153: 20% bucket 155: 20% bucket 148: 70% bucket 146: 80% Sorting block time: 00:00:01 Returning block of 3389521 for bucket 133 bucket 136: 70% Getting block 161 of 210 Reserving size (4338519) for bucket 161 Calculating Z arrays for bucket 161 Entering block accumulator loop for bucket 161: bucket 157: 20% bucket 144: 90% bucket 156: 20% bucket 139: 100% Sorting block of length 3702436 for bucket 139 (Using difference cover) bucket 135: 100% Sorting block of length 3503044 for bucket 135 (Using difference cover) bucket 138: 100% Sorting block of length 2934771 for bucket 138 (Using difference cover) bucket 140: 100% Sorting block of length 2929218 for bucket 140 (Using difference cover) bucket 158: 20% bucket 147: 80% bucket 152: 30% bucket 151: 40% bucket 145: 90% bucket 159: 20% bucket 154: 30% bucket 160: 20% bucket 141: 100% Sorting block of length 3223573 for bucket 141 (Using difference cover) bucket 155: 30% Sorting block time: 00:00:01 Returning block of 2934772 for bucket 138 bucket 142: 100% Sorting block of length 1288959 for bucket 142 (Using difference cover) bucket 153: 30% bucket 150: 60% Getting block 162 of 210 Reserving size (4338519) for bucket 162 Calculating Z arrays for bucket 162 Entering block accumulator loop for bucket 162: bucket 148: 80% Sorting block time: 00:00:01 Returning block of 2929219 for bucket 140 Sorting block time: 00:00:01 Returning block of 3702437 for bucket 139 Getting block 163 of 210 Reserving size (4338519) for bucket 163 Calculating Z arrays for bucket 163 Entering block accumulator loop for bucket 163: Sorting block time: 00:00:01 Returning block of 3503045 for bucket 135 Getting block 164 of 210 Reserving size (4338519) for bucket 164 Calculating Z arrays for bucket 164 Entering block accumulator loop for bucket 164: Getting block 165 of 210 Reserving size (4338519) for bucket 165 Calculating Z arrays for bucket 165 Entering block accumulator loop for bucket 165: bucket 143: 100% Sorting block of length 3147332 for bucket 143 (Using difference cover) Sorting block time: 00:00:00 Returning block of 1288960 for bucket 142 Getting block 166 of 210 Reserving size (4338519) for bucket 166 Calculating Z arrays for bucket 166 Entering block accumulator loop for bucket 166: bucket 149: 80% bucket 137: 100% Sorting block of length 3093039 for bucket 137 (Using difference cover) bucket 161: 10% bucket 146: 90% bucket 136: 80% bucket 157: 30% Sorting block time: 00:00:01 Returning block of 3223574 for bucket 141 Getting block 167 of 210 Reserving size (4338519) for bucket 167 Calculating Z arrays for bucket 167 Entering block accumulator loop for bucket 167: Sorting block time: 00:00:02 Returning block of 3147333 for bucket 143 Getting block 168 of 210 Reserving size (4338519) for bucket 168 Calculating Z arrays for bucket 168 Entering block accumulator loop for bucket 168: bucket 158: 30% bucket 147: 90% Sorting block time: 00:00:01 Returning block of 3093040 for bucket 137 Getting block 169 of 210 Reserving size (4338519) for bucket 169 Calculating Z arrays for bucket 169 Entering block accumulator loop for bucket 169: bucket 154: 40% bucket 151: 50% bucket 152: 40% bucket 144: 100% Sorting block of length 3704240 for bucket 144 (Using difference cover) bucket 159: 30% bucket 156: 30% bucket 160: 30% bucket 155: 40% bucket 145: 100% Sorting block of length 755052 for bucket 145 (Using difference cover) bucket 148: 90% bucket 153: 40% Sorting block time: 00:00:00 Returning block of 755053 for bucket 145 Getting block 170 of 210 Reserving size (4338519) for bucket 170 Calculating Z arrays for bucket 170 Entering block accumulator loop for bucket 170: bucket 165: 10% bucket 150: 70% bucket 162: 10% bucket 161: 20% Sorting block time: 00:00:02 Returning block of 3704241 for bucket 144 Getting block 171 of 210 Reserving size (4338519) for bucket 171 Calculating Z arrays for bucket 171 Entering block accumulator loop for bucket 171: bucket 163: 10% bucket 164: 10% bucket 166: 10% bucket 157: 40% bucket 136: 90% bucket 149: 90% bucket 146: 100% Sorting block of length 4071777 for bucket 146 (Using difference cover) bucket 158: 40% bucket 147: 100% Sorting block of length 2856143 for bucket 147 (Using difference cover) bucket 154: 50% bucket 167: 10% bucket 151: 60% bucket 152: 50% bucket 159: 40% bucket 168: 10% bucket 160: 40% bucket 155: 50% bucket 156: 40% bucket 169: 10% bucket 148: 100% Sorting block of length 4050905 for bucket 148 (Using difference cover) bucket 165: 20% Sorting block time: 00:00:01 Returning block of 2856144 for bucket 147 bucket 153: 50% Getting block 172 of 210 Reserving size (4338519) for bucket 172 Calculating Z arrays for bucket 172 Entering block accumulator loop for bucket 172: Sorting block time: 00:00:02 Returning block of 4071778 for bucket 146 Getting block 173 of 210 Reserving size (4338519) for bucket 173 Calculating Z arrays for bucket 173 Entering block accumulator loop for bucket 173: bucket 161: 30% bucket 170: 10% bucket 136: 100% Sorting block of length 3541126 for bucket 136 (Using difference cover) bucket 150: 80% bucket 157: 50% bucket 166: 20% bucket 162: 20% bucket 171: 10% bucket 163: 20% bucket 164: 20% bucket 158: 50% bucket 149: 100% Sorting block of length 4182099 for bucket 149 (Using difference cover) bucket 154: 60% bucket 151: 70% Sorting block time: 00:00:01 Returning block of 4050906 for bucket 148 bucket 159: 50% bucket 168: 20% bucket 152: 60% Getting block 174 of 210 Reserving size (4338519) for bucket 174 Calculating Z arrays for bucket 174 Entering block accumulator loop for bucket 174: bucket 160: 50% bucket 167: 20% bucket 155: 60% bucket 156: 50% bucket 165: 30% bucket 172: 10% bucket 169: 20% bucket 153: 60% bucket 161: 40% bucket 173: 10% bucket 170: 20% bucket 150: 90% bucket 166: 30% bucket 157: 60% bucket 162: 30% bucket 158: 60% bucket 171: 20% bucket 154: 70% bucket 164: 30% bucket 163: 30% Sorting block time: 00:00:01 Returning block of 3541127 for bucket 136 bucket 151: 80% bucket 159: 60% bucket 168: 30% bucket 152: 70% Getting block 175 of 210 Reserving size (4338519) for bucket 175 Calculating Z arrays for bucket 175 Entering block accumulator loop for bucket 175: bucket 160: 60% bucket 174: 10% bucket 155: 70% bucket 167: 30% Sorting block time: 00:00:02 Returning block of 4182100 for bucket 149 Getting block 176 of 210 Reserving size (4338519) for bucket 176 Calculating Z arrays for bucket 176 Entering block accumulator loop for bucket 176: bucket 165: 40% bucket 172: 20% bucket 156: 60% bucket 153: 70% bucket 161: 50% bucket 169: 30% bucket 173: 20% bucket 170: 30% bucket 154: 80% bucket 158: 70% bucket 166: 40% bucket 150: 100% Sorting block of length 4070473 for bucket 150 (Using difference cover) bucket 157: 70% bucket 151: 90% bucket 159: 70% bucket 162: 40% bucket 164: 40% bucket 171: 30% bucket 163: 40% bucket 152: 80% bucket 175: 10% bucket 174: 20% bucket 160: 70% bucket 155: 80% bucket 168: 40% bucket 176: 10% bucket 165: 50% bucket 167: 40% bucket 172: 30% Sorting block time: 00:00:01 Returning block of 4070474 for bucket 150 Getting block 177 of 210 Reserving size (4338519) for bucket 177 Calculating Z arrays for bucket 177 Entering block accumulator loop for bucket 177: bucket 161: 60% bucket 156: 70% bucket 153: 80% bucket 154: 90% bucket 158: 80% bucket 169: 40% bucket 173: 30% bucket 151: 100% Sorting block of length 3713020 for bucket 151 (Using difference cover) bucket 170: 40% bucket 159: 80% bucket 175: 20% bucket 152: 90% bucket 174: 30% bucket 160: 80% bucket 166: 50% bucket 155: 90% bucket 157: 80% bucket 162: 50% bucket 164: 50% bucket 176: 20% bucket 171: 40% bucket 163: 50% bucket 165: 60% bucket 172: 40% bucket 168: 50% bucket 161: 70% Sorting block time: 00:00:01 Returning block of 3713021 for bucket 151 Getting block 178 of 210 Reserving size (4338519) for bucket 178 Calculating Z arrays for bucket 178 Entering block accumulator loop for bucket 178: bucket 167: 50% bucket 153: 90% bucket 177: 10% bucket 154: 100% Sorting block of length 1184266 for bucket 154 (Using difference cover) bucket 158: 90% bucket 156: 80% Sorting block time: 00:00:00 Returning block of 1184267 for bucket 154 Getting block 179 of 210 Reserving size (4338519) for bucket 179 Calculating Z arrays for bucket 179 Entering block accumulator loop for bucket 179: bucket 159: 90% bucket 175: 30% bucket 174: 40% bucket 160: 90% bucket 155: 100% Sorting block of length 3983998 for bucket 155 (Using difference cover) bucket 152: 100% Sorting block of length 3383067 for bucket 152 (Using difference cover) bucket 169: 50% bucket 173: 40% bucket 176: 30% bucket 170: 50% bucket 166: 60% bucket 165: 70% bucket 172: 50% bucket 157: 90% bucket 164: 60% bucket 162: 60% bucket 161: 80% bucket 163: 60% bucket 171: 50% bucket 178: 10% bucket 168: 60% bucket 158: 100% Sorting block of length 3478279 for bucket 158 (Using difference cover) bucket 153: 100% Sorting block of length 4071018 for bucket 153 (Using difference cover) bucket 167: 60% bucket 177: 20% Sorting block time: 00:00:01 Returning block of 3383068 for bucket 152 bucket 156: 90% bucket 179: 10% Getting block 180 of 210 Reserving size (4338519) for bucket 180 Calculating Z arrays for bucket 180 Entering block accumulator loop for bucket 180: bucket 159: 100% Sorting block of length 4288216 for bucket 159 (Using difference cover) bucket 175: 40% bucket 160: 100% Sorting block of length 2555883 for bucket 160 (Using difference cover) bucket 174: 50% Sorting block time: 00:00:01 Returning block of 3983999 for bucket 155 Getting block 181 of 210 Reserving size (4338519) for bucket 181 Calculating Z arrays for bucket 181 Entering block accumulator loop for bucket 181: bucket 173: 50% bucket 176: 40% bucket 169: 60% bucket 170: 60% bucket 166: 70% bucket 165: 80% bucket 172: 60% bucket 157: 100% Sorting block of length 3963976 for bucket 157 (Using difference cover) bucket 161: 90% bucket 164: 70% bucket 178: 20% bucket 162: 70% bucket 163: 70% bucket 171: 60% bucket 168: 70% bucket 167: 70% Sorting block time: 00:00:02 Returning block of 2555884 for bucket 160 Getting block 182 of 210 Reserving size (4338519) for bucket 182 Calculating Z arrays for bucket 182 Entering block accumulator loop for bucket 182: bucket 180: 10% bucket 179: 20% bucket 177: 30% bucket 156: 100% Sorting block of length 3702877 for bucket 156 (Using difference cover) Sorting block time: 00:00:02 Returning block of 3478280 for bucket 158 bucket 175: 50% bucket 181: 10% Getting block 183 of 210 Reserving size (4338519) for bucket 183 Calculating Z arrays for bucket 183 Entering block accumulator loop for bucket 183: bucket 174: 60% bucket 173: 60% bucket 176: 50% bucket 166: 80% Sorting block time: 00:00:02 Returning block of 4071019 for bucket 153 bucket 170: 70% bucket 165: 90% bucket 169: 70% bucket 172: 70% Getting block 184 of 210 Reserving size (4338519) for bucket 184 Calculating Z arrays for bucket 184 Entering block accumulator loop for bucket 184: Sorting block time: 00:00:02 Returning block of 4288217 for bucket 159 bucket 161: 100% Sorting block of length 2355865 for bucket 161 (Using difference cover) bucket 164: 80% bucket 178: 30% bucket 162: 80% Getting block 185 of 210 Reserving size (4338519) for bucket 185 Calculating Z arrays for bucket 185 Entering block accumulator loop for bucket 185: bucket 163: 80% bucket 171: 70% bucket 168: 80% Sorting block time: 00:00:02 Returning block of 3963977 for bucket 157 Getting block 186 of 210 Reserving size (4338519) for bucket 186 Calculating Z arrays for bucket 186 Entering block accumulator loop for bucket 186: Sorting block time: 00:00:01 Returning block of 3702878 for bucket 156 bucket 177: 40% Sorting block time: 00:00:01 Returning block of 2355866 for bucket 161 Getting block 187 of 210 Reserving size (4338519) for bucket 187 Calculating Z arrays for bucket 187 Entering block accumulator loop for bucket 187: Getting block 188 of 210 Reserving size (4338519) for bucket 188 Calculating Z arrays for bucket 188 Entering block accumulator loop for bucket 188: bucket 174: 70% bucket 167: 80% bucket 166: 90% bucket 176: 60% bucket 173: 70% bucket 170: 80% bucket 169: 80% bucket 182: 10% bucket 180: 20% bucket 179: 30% bucket 164: 90% bucket 162: 90% bucket 163: 90% bucket 175: 60% bucket 171: 80% bucket 181: 20% bucket 183: 10% bucket 168: 90% bucket 186: 10% bucket 177: 50% bucket 187: 10% bucket 174: 80% bucket 166: 100% Sorting block of length 1688606 for bucket 166 (Using difference cover) bucket 176: 70% bucket 170: 90% bucket 173: 80% bucket 165: 100% Sorting block of length 3664620 for bucket 165 (Using difference cover) bucket 169: 90% bucket 164: 100% Sorting block of length 2255722 for bucket 164 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1688607 for bucket 166 Getting block 189 of 210 Reserving size (4338519) for bucket 189 Calculating Z arrays for bucket 189 Entering block accumulator loop for bucket 189: bucket 162: 100% Sorting block of length 3177518 for bucket 162 (Using difference cover) bucket 163: 100% Sorting block of length 3890047 for bucket 163 (Using difference cover) bucket 184: 10% bucket 172: 80% bucket 171: 90% bucket 168: 100% Sorting block of length 2696845 for bucket 168 (Using difference cover) bucket 186: 20% bucket 185: 10% bucket 178: 40% bucket 187: 20% bucket 177: 60% Sorting block time: 00:00:01 Returning block of 2255723 for bucket 164 Getting block 190 of 210 Reserving size (4338519) for bucket 190 Calculating Z arrays for bucket 190 Entering block accumulator loop for bucket 190: bucket 174: 90% Sorting block time: 00:00:01 Returning block of 3664621 for bucket 165 Getting block 191 of 210 Reserving size (4338519) for bucket 191 Calculating Z arrays for bucket 191 Entering block accumulator loop for bucket 191: Sorting block time: 00:00:01 Returning block of 3177519 for bucket 162 Getting block 192 of 210 Reserving size (4338519) for bucket 192 Calculating Z arrays for bucket 192 Entering block accumulator loop for bucket 192: bucket 167: 90% Sorting block time: 00:00:02 Returning block of 3890048 for bucket 163 bucket 188: 10% bucket 170: 100% Sorting block of length 3646349 for bucket 170 (Using difference cover) bucket 176: 80% Sorting block time: 00:00:01 Returning block of 2696846 for bucket 168 Getting block 193 of 210 Reserving size (4338519) for bucket 193 Calculating Z arrays for bucket 193 Entering block accumulator loop for bucket 193: bucket 173: 90% Getting block 194 of 210 Reserving size (4338519) for bucket 194 Calculating Z arrays for bucket 194 Entering block accumulator loop for bucket 194: bucket 180: 30% bucket 182: 20% bucket 169: 100% Sorting block of length 3357051 for bucket 169 (Using difference cover) bucket 179: 40% bucket 181: 30% bucket 175: 70% bucket 189: 10% bucket 183: 20% bucket 171: 100% Sorting block of length 2179366 for bucket 171 (Using difference cover) Sorting block time: 00:00:01 Returning block of 3646350 for bucket 170 Getting block 195 of 210 Reserving size (4338519) for bucket 195 Calculating Z arrays for bucket 195 Entering block accumulator loop for bucket 195: bucket 186: 30% bucket 184: 20% bucket 172: 90% Sorting block time: 00:00:01 Returning block of 2179367 for bucket 171 bucket 187: 30% bucket 177: 70% Getting block 196 of 210 Reserving size (4338519) for bucket 196 Calculating Z arrays for bucket 196 Entering block accumulator loop for bucket 196: Sorting block time: 00:00:02 Returning block of 3357052 for bucket 169 Getting block 197 of 210 Reserving size (4338519) for bucket 197 Calculating Z arrays for bucket 197 Entering block accumulator loop for bucket 197: bucket 190: 10% bucket 185: 20% bucket 178: 50% bucket 191: 10% bucket 174: 100% Sorting block of length 2217196 for bucket 174 (Using difference cover) bucket 188: 20% bucket 192: 10% bucket 167: 100% Sorting block of length 4004464 for bucket 167 (Using difference cover) bucket 194: 10% bucket 176: 90% bucket 193: 10% Sorting block time: 00:00:01 Returning block of 2217197 for bucket 174 bucket 173: 100% Sorting block of length 2190046 for bucket 173 (Using difference cover) bucket 180: 40% Getting block 198 of 210 Reserving size (4338519) for bucket 198 Calculating Z arrays for bucket 198 Entering block accumulator loop for bucket 198: bucket 189: 20% bucket 182: 30% bucket 175: 80% bucket 181: 40% bucket 179: 50% bucket 195: 10% bucket 186: 40% Sorting block time: 00:00:01 Returning block of 2190047 for bucket 173 bucket 196: 10% bucket 177: 80% Getting block 199 of 210 Reserving size (4338519) for bucket 199 Calculating Z arrays for bucket 199 Entering block accumulator loop for bucket 199: bucket 190: 20% bucket 197: 10% bucket 187: 40% Sorting block time: 00:00:01 Returning block of 4004465 for bucket 167 Getting block 200 of 210 Reserving size (4338519) for bucket 200 Calculating Z arrays for bucket 200 Entering block accumulator loop for bucket 200: bucket 183: 30% bucket 192: 20% bucket 194: 20% bucket 193: 20% bucket 176: 100% Sorting block of length 2396380 for bucket 176 (Using difference cover) bucket 189: 30% bucket 184: 30% bucket 172: 100% Sorting block of length 3608660 for bucket 172 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2396381 for bucket 176 bucket 195: 20% Getting block 201 of 210 Reserving size (4338519) for bucket 201 Calculating Z arrays for bucket 201 Entering block accumulator loop for bucket 201: bucket 186: 50% bucket 196: 20% bucket 190: 30% bucket 185: 30% bucket 197: 20% bucket 177: 90% bucket 199: 10% bucket 187: 50% bucket 200: 10% bucket 178: 60% bucket 191: 20% bucket 192: 30% bucket 188: 30% bucket 194: 30% bucket 193: 30% bucket 175: 90% Sorting block time: 00:00:02 Returning block of 3608661 for bucket 172 Getting block 202 of 210 Reserving size (4338519) for bucket 202 Calculating Z arrays for bucket 202 Entering block accumulator loop for bucket 202: bucket 189: 40% bucket 180: 50% bucket 198: 10% bucket 182: 40% bucket 195: 30% bucket 201: 10% bucket 181: 50% bucket 179: 60% bucket 190: 40% bucket 196: 30% bucket 186: 60% bucket 197: 30% bucket 177: 100% Sorting block of length 2625065 for bucket 177 (Using difference cover) bucket 199: 20% bucket 187: 60% bucket 200: 20% bucket 183: 40% bucket 192: 40% bucket 193: 40% bucket 194: 40% Sorting block time: 00:00:01 Returning block of 2625066 for bucket 177 Getting block 203 of 210 Reserving size (4338519) for bucket 203 Calculating Z arrays for bucket 203 Entering block accumulator loop for bucket 203: bucket 189: 50% bucket 184: 40% bucket 195: 40% bucket 201: 20% bucket 190: 50% bucket 196: 40% bucket 197: 40% bucket 186: 70% bucket 199: 30% bucket 200: 30% bucket 187: 70% bucket 185: 40% bucket 178: 70% bucket 191: 30% bucket 192: 50% bucket 193: 50% bucket 194: 50% bucket 203: 10% bucket 189: 60% bucket 188: 40% bucket 175: 100% Sorting block of length 2978131 for bucket 175 (Using difference cover) bucket 202: 10% bucket 180: 60% bucket 195: 50% bucket 201: 30% bucket 198: 20% bucket 190: 60% bucket 182: 50% bucket 181: 60% bucket 197: 50% bucket 196: 50% bucket 186: 80% bucket 199: 40% bucket 200: 40% bucket 187: 80% bucket 179: 70% Sorting block time: 00:00:01 Returning block of 2978132 for bucket 175 Getting block 204 of 210 Reserving size (4338519) for bucket 204 Calculating Z arrays for bucket 204 Entering block accumulator loop for bucket 204: bucket 192: 60% bucket 193: 60% bucket 183: 50% bucket 194: 60% bucket 203: 20% bucket 189: 70% bucket 195: 60% bucket 201: 40% bucket 190: 70% bucket 197: 60% bucket 184: 50% bucket 196: 60% bucket 186: 90% bucket 185: 50% bucket 199: 50% bucket 200: 50% bucket 187: 90% bucket 191: 40% bucket 178: 80% bucket 188: 50% bucket 192: 70% bucket 193: 70% bucket 202: 20% bucket 194: 70% bucket 203: 30% bucket 189: 80% bucket 180: 70% bucket 198: 30% bucket 181: 70% bucket 182: 60% bucket 195: 70% bucket 190: 80% bucket 201: 50% bucket 204: 10% bucket 179: 80% bucket 197: 70% bucket 196: 70% bucket 186: 100% Sorting block of length 3980486 for bucket 186 (Using difference cover) bucket 200: 60% bucket 199: 60% bucket 183: 60% bucket 187: 100% Sorting block of length 2737569 for bucket 187 (Using difference cover) bucket 193: 80% bucket 188: 60% bucket 192: 80% bucket 203: 40% bucket 189: 90% Sorting block time: 00:00:02 Returning block of 2737570 for bucket 187 Getting block 205 of 210 Reserving size (4338519) for bucket 205 Calculating Z arrays for bucket 205 Entering block accumulator loop for bucket 205: Sorting block time: 00:00:02 Returning block of 3980487 for bucket 186 Getting block 206 of 210 Reserving size (4338519) for bucket 206 Calculating Z arrays for bucket 206 Entering block accumulator loop for bucket 206: bucket 190: 90% bucket 201: 60% bucket 195: 80% bucket 184: 60% bucket 197: 80% bucket 196: 80% bucket 200: 70% bucket 199: 70% bucket 185: 60% bucket 193: 90% bucket 194: 80% bucket 188: 70% bucket 192: 90% bucket 191: 50% bucket 178: 90% bucket 203: 50% bucket 189: 100% Sorting block of length 1840313 for bucket 189 (Using difference cover) bucket 205: 10% bucket 190: 100% Sorting block of length 2807965 for bucket 190 (Using difference cover) bucket 201: 70% Sorting block time: 00:00:01 Returning block of 1840314 for bucket 189 bucket 202: 30% bucket 180: 80% bucket 195: 90% Getting block 207 of 210 Reserving size (4338519) for bucket 207 Calculating Z arrays for bucket 207 Entering block accumulator loop for bucket 207: bucket 181: 80% bucket 197: 90% bucket 198: 40% bucket 182: 70% bucket 196: 90% bucket 200: 80% bucket 199: 80% bucket 193: 100% Sorting block of length 4214907 for bucket 193 (Using difference cover) bucket 204: 20% bucket 194: 90% bucket 188: 80% bucket 179: 90% Sorting block time: 00:00:01 Returning block of 2807966 for bucket 190 bucket 192: 100% Sorting block of length 2084346 for bucket 192 (Using difference cover) Getting block 208 of 210 Reserving size (4338519) for bucket 208 Calculating Z arrays for bucket 208 Entering block accumulator loop for bucket 208: bucket 203: 60% bucket 183: 70% Sorting block time: 00:00:01 Returning block of 2084347 for bucket 192 Getting block 209 of 210 Reserving size (4338519) for bucket 209 Calculating Z arrays for bucket 209 Entering block accumulator loop for bucket 209: bucket 205: 20% bucket 201: 80% bucket 207: 10% bucket 195: 100% Sorting block of length 2810601 for bucket 195 (Using difference cover) bucket 206: 10% bucket 197: 100% Sorting block of length 3125559 for bucket 197 (Using difference cover) bucket 184: 70% bucket 196: 100% Sorting block of length 3937653 for bucket 196 (Using difference cover) bucket 185: 70% bucket 200: 90% bucket 178: 100% Sorting block of length 2703119 for bucket 178 (Using difference cover) bucket 191: 60% bucket 199: 90% bucket 204: 30% bucket 188: 90% bucket 194: 100% Sorting block of length 1787812 for bucket 194 (Using difference cover) Sorting block time: 00:00:02 Returning block of 4214908 for bucket 193 bucket 180: 90% bucket 202: 40% bucket 181: 90% Getting block 210 of 210 Reserving size (4338519) for bucket 210 Calculating Z arrays for bucket 210 Entering block accumulator loop for bucket 210: bucket 203: 70% bucket 182: 80% bucket 198: 50% bucket 179: 100% Sorting block of length 2259699 for bucket 179 (Using difference cover) bucket 208: 10% bucket 183: 80% bucket 209: 10% bucket 201: 90% bucket 205: 30% bucket 207: 20% bucket 206: 20% bucket 184: 80% bucket 185: 80% bucket 210: 10% Sorting block time: 00:00:01 Returning block of 1787813 for bucket 194 bucket 200: 100% Sorting block of length 4105870 for bucket 200 (Using difference cover) bucket 191: 70% bucket 199: 100% Sorting block of length 3974044 for bucket 199 (Using difference cover) bucket 188: 100% Sorting block of length 4305083 for bucket 188 (Using difference cover) Sorting block time: 00:00:02 Returning block of 2810602 for bucket 195 bucket 204: 40% bucket 180: 100% Sorting block of length 3461609 for bucket 180 (Using difference cover) bucket 181: 100% Sorting block of length 3292672 for bucket 181 (Using difference cover) bucket 202: 50% bucket 203: 80% bucket 182: 90% bucket 198: 60% Sorting block time: 00:00:01 Returning block of 3125560 for bucket 197 bucket 208: 20% Sorting block time: 00:00:01 Returning block of 2703120 for bucket 178 bucket 209: 20% bucket 183: 90% bucket 201: 100% Sorting block of length 1476525 for bucket 201 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2259700 for bucket 179 bucket 207: 30% Sorting block time: 00:00:01 Returning block of 3937654 for bucket 196 bucket 205: 40% bucket 210: 20% bucket 206: 30% bucket 184: 90% Sorting block time: 00:00:01 Returning block of 1476526 for bucket 201 bucket 185: 90% bucket 191: 80% bucket 204: 50% Sorting block time: 00:00:01 Returning block of 3292673 for bucket 181 bucket 202: 60% Sorting block time: 00:00:01 Returning block of 3461610 for bucket 180 bucket 182: 100% Sorting block of length 2910235 for bucket 182 (Using difference cover) bucket 203: 90% bucket 198: 70% Sorting block time: 00:00:02 Returning block of 3974045 for bucket 199 bucket 208: 30% Sorting block time: 00:00:02 Returning block of 4105871 for bucket 200 bucket 210: 30% Sorting block time: 00:00:02 Returning block of 4305084 for bucket 188 bucket 183: 100% Sorting block of length 3374728 for bucket 183 (Using difference cover) bucket 209: 30% bucket 184: 100% Sorting block of length 3247634 for bucket 184 (Using difference cover) bucket 207: 40% bucket 205: 50% bucket 206: 40% Sorting block time: 00:00:02 Returning block of 2910236 for bucket 182 bucket 185: 100% Sorting block of length 2873025 for bucket 185 (Using difference cover) bucket 191: 90% bucket 204: 60% bucket 210: 40% bucket 202: 70% Sorting block time: 00:00:02 Returning block of 3374729 for bucket 183 bucket 203: 100% Sorting block of length 1838701 for bucket 203 (Using difference cover) bucket 198: 80% bucket 208: 40% Sorting block time: 00:00:01 Returning block of 3247635 for bucket 184 Sorting block time: 00:00:01 Returning block of 2873026 for bucket 185 bucket 209: 40% Sorting block time: 00:00:00 Returning block of 1838702 for bucket 203 bucket 206: 50% bucket 205: 60% bucket 207: 50% bucket 191: 100% Sorting block of length 2626704 for bucket 191 (Using difference cover) bucket 210: 50% bucket 204: 70% bucket 202: 80% Sorting block time: 00:00:01 Returning block of 2626705 for bucket 191 bucket 198: 90% bucket 208: 50% bucket 209: 50% bucket 210: 60% bucket 206: 60% bucket 205: 70% bucket 207: 60% bucket 204: 80% bucket 210: 70% bucket 208: 60% bucket 209: 60% bucket 206: 70% bucket 205: 80% bucket 202: 90% bucket 210: 80% bucket 208: 70% bucket 198: 100% Sorting block of length 3807997 for bucket 198 (Using difference cover) bucket 209: 70% bucket 206: 80% bucket 210: 90% bucket 205: 90% Sorting block time: 00:00:02 Returning block of 3807998 for bucket 198 bucket 207: 70% bucket 204: 90% bucket 208: 80% bucket 209: 80% bucket 210: 100% Sorting block of length 663372 for bucket 210 (Using difference cover) bucket 202: 100% Sorting block of length 2919051 for bucket 202 (Using difference cover) Sorting block time: 00:00:00 Returning block of 663373 for bucket 210 bucket 206: 90% Sorting block time: 00:00:01 Returning block of 2919052 for bucket 202 bucket 205: 100% Sorting block of length 4597545 for bucket 205 (Using difference cover) bucket 208: 90% bucket 207: 80% bucket 204: 100% Sorting block of length 173783 for bucket 204 (Using difference cover) Sorting block time: 00:00:00 Returning block of 173784 for bucket 204 bucket 209: 90% Sorting block time: 00:00:02 Returning block of 4597546 for bucket 205 bucket 206: 100% Sorting block of length 1387376 for bucket 206 (Using difference cover) Sorting block time: 00:00:01 Returning block of 1387377 for bucket 206 bucket 208: 100% Sorting block of length 2951119 for bucket 208 (Using difference cover) bucket 207: 90% bucket 209: 100% Sorting block of length 3710744 for bucket 209 (Using difference cover) bucket 207: 100% Sorting block of length 3911969 for bucket 207 (Using difference cover) Sorting block time: 00:00:01 Returning block of 2951120 for bucket 208 Sorting block time: 00:00:02 Returning block of 3710745 for bucket 209 Sorting block time: 00:00:02 Returning block of 3911970 for bucket 207 Exited Ebwt loop fchr[A]: 0 fchr[C]: 215403148 fchr[G]: 215403148 fchr[T]: 323920226 fchr[$]: 647885551 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 220173300 bytes to primary EBWT file: BS_CT.rev.1.bt2 Wrote 161971392 bytes to secondary EBWT file: BS_CT.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 647885551 bwtLen: 647885552 sz: 161971388 bwtSz: 161971388 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 40492847 offsSz: 161971388 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3374404 numLines: 3374404 ebwtTotLen: 215961856 ebwtTotSz: 215961856 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:04:01 Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_10_R1.fastp-trim.20201202.fq.gz to zr3534_10_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R1.fastp-trim.20201202.fq.gz to zr3534_10_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R1.fastp-trim.20201202.fq.gz (77576026 sequences in total) Writing a C -> T converted version of the input file zr3534_10_R2.fastp-trim.20201202.fq.gz to zr3534_10_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R2.fastp-trim.20201202.fq.gz to zr3534_10_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R2.fastp-trim.20201202.fq.gz (77576026 sequences in total) Input files are zr3534_10_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_10_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_10_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 77 * 0 0 * * 0 0 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 141 * 0 0 * * 0 0 ATTTATATATCCATAATTATAACATCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATCTCT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_10_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 99 NC_047564.1_GA_converted 7169120 0 1M5I100M1I8M = 7169121 109 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF AS:i:-52 XN:i:0 XM:i:4 XO:i:2 XG:i:6 NM:i:10 MD:Z:91A11T1C1T1 YS:i:-62 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 147 NC_047564.1_GA_converted 7169121 0 96M11I6M = 7169120 -109 AAAAACATACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATTATAATTATAAATATATAAAT ,,,,F,F,,,,,F,F,:,::F:FFF:F,F,F,FFFFF:FFF:FFFFF:FFFFF:::F:F,F:FF:::,F:FFFFF:F:F:,FFFFFF:FFFFFFFFFFFF:FFFFF:FFFFFF AS:i:-62 XN:i:0 XM:i:4 XO:i:1 XG:i:11 NM:i:15 MD:Z:5A1A1A1A90 YS:i:-52 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_10_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 83 NC_047567.1_CT_converted 9852871 0 4M1I5M2I103M = 9852871 -112 ATATATATATTATTATAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT FF:F:FF,FF,,:F,,,:,FF:FFFFFFFFFFFFF:F,F,FFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-55 XN:i:0 XM:i:6 XO:i:2 XG:i:3 NM:i:9 MD:Z:2T3A95G2A0A3A1 YS:i:-63 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 163 NC_047567.1_CT_converted 9852871 0 4M1I11M4I81M7I5M = 9852871 -112 ATTTATATATTTATAATTATAATATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGTATGTTTTT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, AS:i:-63 XN:i:0 XM:i:2 XO:i:3 XG:i:12 NM:i:14 MD:Z:6A11T82 YS:i:-55 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_10_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 77 * 0 0 * * 0 0 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 141 * 0 0 * * 0 0 ATTTATATATCCATAATTATAACATCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATCTCT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, YT:Z:UP >>> Writing bisulfite mapping results to zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1103:8820:7341_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1109:29225:3537_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1114:15926:13667_1:N:0:ACAACTAC+TGTGATAA NW_022994933.1 29880 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1116:2230:36323_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1119:6072:21120_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18122 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1127:12274:3959_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1128:21757:10113_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1137:15338:19257_1:N:0:ACAACTAC+TGTGATAA NW_022994978.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1146:24460:20838_1:N:0:ACAACTAC+TGTGATAA NW_022994980.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1146:24252:20885_1:N:0:ACAACTAC+TGTGATAA NW_022994980.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1146:25581:24251_1:N:0:ACAACTAC+TGTGATAA NW_022994980.1 2 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1150:16098:33661_1:N:0:ACAACTAC+TGTGATAA NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1152:27688:27680_1:N:0:ACAACTAC+TGTGATAA NW_022994978.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1214:18358:36072_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18117 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1219:29803:19163_1:N:0:ACAACTAC+TGTGATAA NW_022994934.1 161480 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1219:31051:32565_1:N:0:ACAACTAC+TGTGATAA NW_022994934.1 161480 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1221:11885:26897_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 324540 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1225:9661:17722_1:N:0:ACAACTAC+TGTGATAA NW_022994931.1 1 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1247:18765:28667_1:N:0:ACAACTAC+TGTGATAA NW_022994898.1 63851 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1255:17264:26819_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1256:3197:10347_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1258:3830:5932_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18116 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1273:30472:26866_1:N:0:ACAACTAC+TGTGATAA NW_022994937.1 490594 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1274:27805:15421_1:N:0:ACAACTAC+TGTGATAA NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1274:3640:18286_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 1 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1315:30508:11459_1:N:0:ACAACTAC+TGTGATAA NW_022994817.1 2139 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1347:26151:24173_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 297105 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1347:27579:24925_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 297105 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1365:15329:25880_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1371:4752:2080_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 324539 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1371:6515:5509_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 324539 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1406:1461:21684_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1410:23104:34773_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1417:19958:21809_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1419:21549:12947_1:N:0:ACAACTAC+TGTGATAA NW_022994786.1 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1426:1841:3709_1:N:0:ACAACTAC+TGTGATAA NW_022994965.1 30579 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1431:17996:36636_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1455:2392:21574_1:N:0:ACAACTAC+TGTGATAA NW_022994966.1 514638 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1462:3504:12915_1:N:0:ACAACTAC+TGTGATAA NW_022994987.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1462:6822:26553_1:N:0:ACAACTAC+TGTGATAA NW_022994898.1 63844 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1463:7591:24815_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18119 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1463:7618:25050_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18119 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1470:32425:26365_1:N:0:ACAACTAC+TGTGATAA NW_022994816.1 984966 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1470:30644:31861_1:N:0:ACAACTAC+TGTGATAA NW_022994816.1 984964 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1471:32805:16783_1:N:0:ACAACTAC+TGTGATAA NW_022994817.1 2139 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1475:12789:27336_1:N:0:ACAACTAC+TGTGATAA NW_022994786.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1502:5168:1548_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 333532 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1502:1362:23547_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1504:16703:9283_1:N:0:ACAACTAC+CGTGATAA NW_022994786.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1520:8947:20870_1:N:0:ACAACTAC+TGTGATAA NW_022994964.1 245873 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1525:15890:5682_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18122 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1527:2853:24377_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1531:30020:22482_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1531:30870:22482_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1534:19542:6872_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1544:32099:2660_1:N:0:ACAACTAC+TGTGATAA NW_022994785.1 99453 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1547:9534:5666_1:N:0:ACAACTAC+TGTGATAA NW_022994905.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1547:7925:9580_1:N:0:ACAACTAC+TGTGATAA NW_022994794.1 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1559:31873:16141_1:N:0:ACAACTAC+TGTGATAA NW_022994950.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1561:24858:9784_1:N:0:ACAACTAC+TGTGATAA NW_022994978.1 113593 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1567:5376:12900_1:N:0:ACAACTAC+TGTGATAA NW_022994915.1 1 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1575:27905:7044_1:N:0:ACAACTAC+TGTGATAA NW_022994987.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:16577:33802_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:16459:33880_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1630:29948:21981_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18116 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1633:16975:24251_1:N:0:ACAACTAC+TGTGATAA NW_022994898.1 63881 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1644:4517:12132_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 1 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2117:4797:13964_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2120:4264:21652_1:N:0:ACAACTAC+TGTGATAA NW_022994940.1 1 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2126:18656:23375_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2130:20076:18380_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2130:22941:24721_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 2 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2139:18747:33865_1:N:0:ACAACTAC+TGTGATAA NW_022994987.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2140:27362:8390_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2145:21197:31407_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2152:28863:31626_1:N:0:ACAACTAC+TGTGATAA NW_022994978.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:3197:8750_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2162:32850:22529_1:N:0:ACAACTAC+TGTGATAA NW_022994936.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2178:7581:13620_1:N:0:ACAACTAC+TGTGATAA NW_022994898.1 63868 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2218:32714:5290_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 2 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2250:31430:20541_1:N:0:ACAACTAC+TGTGATAA NW_022994919.1 1 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2306:28402:6277_1:N:0:ACAACTAC+TGTGATAA NW_022994998.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2312:27733:5713_1:N:0:ACAACTAC+TGTGATAA NW_022994911.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2313:12771:10269_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2314:16839:14873_1:N:0:ACAACTAC+TGTGATAA NW_022994952.1 218898 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2314:20085:21840_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18122 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2320:6036:5274_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2323:10836:25394_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18110 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2327:5556:12555_1:N:0:ACAACTAC+TGTGATAA NW_022994944.1 261203 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2332:20401:6856_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2346:1777:31563_1:N:0:ACAACTAC+TGTGATAA NW_022994893.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2347:22779:35086_1:N:0:ACAACTAC+TGTGATAA NW_022994997.1 297105 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2348:13512:33004_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2363:22860:2879_1:N:0:ACAACTAC+TGTGATAA NW_022994899.1 3 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:17544:28025_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 324545 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2369:7880:20556_1:N:0:ACAACTAC+TGTGATAA NW_022994980.1 6451 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2374:4951:32925_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18117 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2376:22073:30358_1:N:0:ACAACTAC+TGTGATAA NW_022994817.1 2147 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2405:19090:30201_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2405:18231:30405_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2405:18096:31140_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18126 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2410:12915:9862_1:N:0:ACAACTAC+TGTGATAA NW_022994989.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2410:12156:10081_1:N:0:ACAACTAC+TGTGATAA NW_022994989.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2410:18683:34507_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18110 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2425:32588:5509_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2425:11342:23484_1:N:0:ACAACTAC+TGTGATAA NW_022994956.1 433830 Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2455:16866:26318_1:N:0:ACAACTAC+TGTGATAA NW_022994881.1 520545 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:20528:14779_1:N:0:ACAACTAC+TGTGATAA NW_022994919.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:16206:15906_1:N:0:ACAACTAC+TGTGATAA NW_022994956.1 433829 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:6298:3630_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 333532 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2503:31015:30217_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18111 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2535:2709:1924_1:N:0:ACAACTAC+TGTGATAA NW_022994971.1 30273 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2549:12979:7780_1:N:0:ACAACTAC+TGTGATAA NW_022994962.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2549:12355:8359_1:N:0:ACAACTAC+TGTGATAA NW_022994962.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2549:12373:8359_1:N:0:ACAACTAC+TGTGATAA NW_022994962.1 1 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2555:8992:15060_1:N:0:ACAACTAC+TGTGATAA NW_022994881.1 520519 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2577:8811:26428_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2607:27371:32236_1:N:0:ACAACTAC+TGTGATAA NW_022994946.1 2 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2612:25889:11663_1:N:0:ACAACTAC+TGTGATAA NW_022994819.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2613:16441:28902_1:N:0:ACAACTAC+TGTGATAA NW_022994939.1 3 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2636:1561:36730_1:N:0:ACAACTAC+TGTGATAA NW_022994948.1 858096 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2638:29306:24471_1:N:0:ACAACTAC+TGTGATAA NW_022994962.1 1 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2677:6036:28729_1:N:0:ACAACTAC+TGTGATAA NC_001276.1 1 77576026 reads; of these: 77576026 (100.00%) were paired; of these: 56613286 (72.98%) aligned concordantly 0 times 9498098 (12.24%) aligned concordantly exactly 1 time 11464642 (14.78%) aligned concordantly >1 times 27.02% overall alignment rate 77576026 reads; of these: 77576026 (100.00%) were paired; of these: 56634280 (73.00%) aligned concordantly 0 times 9476704 (12.22%) aligned concordantly exactly 1 time 11465042 (14.78%) aligned concordantly >1 times 27.00% overall alignment rate 77576026 reads; of these: 77576026 (100.00%) were paired; of these: 56641569 (73.01%) aligned concordantly 0 times 9487214 (12.23%) aligned concordantly exactly 1 time 11447243 (14.76%) aligned concordantly >1 times 26.99% overall alignment rate 77576026 reads; of these: 77576026 (100.00%) were paired; of these: 56639830 (73.01%) aligned concordantly 0 times 9483740 (12.23%) aligned concordantly exactly 1 time 11452456 (14.76%) aligned concordantly >1 times 26.99% overall alignment rate Processed 77576026 sequences in total Successfully deleted the temporary files zr3534_10_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_10_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_10_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_10_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 77576026 Number of paired-end alignments with a unique best hit: 48007674 Mapping efficiency: 61.9% Sequence pairs with no alignments under any condition: 16783783 Sequence pairs did not map uniquely: 12784569 Sequence pairs which were discarded because genomic sequence could not be extracted: 123 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11986262 ((converted) top strand) GA/CT/CT: 11977878 (complementary to (converted) top strand) GA/CT/GA: 12029411 (complementary to (converted) bottom strand) CT/GA/GA: 12014000 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1687130988 Total methylated C's in CpG context: 22194995 Total methylated C's in CHG context: 1322680 Total methylated C's in CHH context: 5572782 Total methylated C's in Unknown context: 51737 Total unmethylated C's in CpG context: 200864245 Total unmethylated C's in CHG context: 297108560 Total unmethylated C's in CHH context: 1160067726 Total unmethylated C's in Unknown context: 4034330 C methylated in CpG context: 10.0% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 16h 12m 30s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_1_R1.fastp-trim.20201202.fq.gz to zr3534_1_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R1.fastp-trim.20201202.fq.gz to zr3534_1_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R1.fastp-trim.20201202.fq.gz (76522716 sequences in total) Writing a C -> T converted version of the input file zr3534_1_R2.fastp-trim.20201202.fq.gz to zr3534_1_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R2.fastp-trim.20201202.fq.gz to zr3534_1_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R2.fastp-trim.20201202.fq.gz (76522716 sequences in total) Input files are zr3534_1_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_1_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_1_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTGATTTGTGTTTTGTGGTAGTTGTAGTTTTTAATTTGGTGTTTTATTAGATTTGTTTTTATTATAGTGTTGTTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAATCAAAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_1_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTAATTTATATTTTATAATAATTATAATTTTTAATCTAATATTTTATTAAATTTATTTTTATTATAATATTATTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAATAATATTATAATAAAAATAAATTTAATAAAATATTAGATTAAAAATTATAATTATTATAAAATATAAATTAATTAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_1_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTAATTTATATTTTATAATAATTATAATTTTTAATCTAATATTTTATTAAATTTATTTTTATTATAATATTATTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAATAATATTATAATAAAAATAAATTTAATAAAATATTAGATTAAAAATTATAATTATTATAAAATATAAATTAATTAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_1_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 83 NC_047565.1_GA_converted 3976990 23 38M1I54M = 3977000 102 ATTTAAAAATAATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAAT F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF AS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:1A0A0A0C50T36 YS:i:-14 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 163 NC_047565.1_GA_converted 3977000 23 28M1I64M = 3976990 -102 AATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAATCAAAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:45T46 YS:i:-38 YT:Z:CP >>> Writing bisulfite mapping results to zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1113:13485:5963_1:N:0:CTCGAATA+TCGACATC NW_022994903.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1130:2510:31234_1:N:0:CTCGAATA+TCGACATC NW_022994973.1 2 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1150:27172:34334_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1152:17092:17534_1:N:0:CTCGAATA+TCGACATC NW_022994993.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1157:21775:14027_1:N:0:CTCGAATA+TCGACATC NW_022994948.1 858110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1157:21432:14058_1:N:0:CTCGAATA+TCGACATC NW_022994948.1 858110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1159:8106:5979_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1159:7961:6355_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1159:30255:16908_1:N:0:CTCGAATA+TCGACATC NW_022994792.1 66675 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1173:21133:16391_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1221:22073:13197_1:N:0:CTCGAATA+TCGACATC NW_022994906.1 24078 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1239:24849:22670_1:N:0:CTCGAATA+TCGACATC NW_022994997.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1241:8160:30906_1:N:0:CTCGAATA+TCGACATC NW_022994812.1 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1252:17571:19805_1:N:0:CTCGAATA+TCGACATC NW_022994994.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1252:18430:20447_1:N:0:CTCGAATA+TCGACATC NW_022994994.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1252:20455:32784_1:N:0:CTCGAATA+TCGACATC NW_022994958.1 2 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1259:29143:13228_1:N:0:CTCGAATA+TCGACATC NW_022994924.1 127737 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1259:27109:30749_1:N:0:CTCGAATA+TCGACATC NW_022994903.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1272:30825:5963_1:N:0:CTCGAATA+TCGACATC NW_022994994.1 3 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1316:12084:1658_1:N:0:CTCGAATA+TCGACATC NW_022994898.1 63843 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1321:30282:16767_1:N:0:CTCGAATA+TCGACATC NW_022994978.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1324:2338:27743_1:N:0:CTCGAATA+TCGACATC NW_022994933.1 29883 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1350:30635:34507_1:N:0:CTCGAATA+TCGACATC NW_022994935.1 43720 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1353:26711:5729_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1357:27028:17049_1:N:0:CTCGAATA+TCGACATC NW_022994875.1 2 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:7591:14575_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:10836:16063_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1408:31638:34741_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18126 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1430:6008:6825_1:N:0:CTCGAATA+TCGACATC NW_022994997.1 1 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1442:29197:33739_1:N:0:CTCGAATA+TCGACATC NW_022994917.1 1 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1473:22173:30718_1:N:0:CTCGAATA+TCGACATC NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1473:23095:34601_1:N:0:CTCGAATA+TCGACATC NW_022994970.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1511:7663:7811_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1515:30490:20854_1:N:0:CTCGAATA+TCGACATC NW_022994817.1 2189 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1553:26856:35227_1:N:0:CTCGAATA+TCGACATC NC_001276.1 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1555:30969:33896_1:N:0:CTCGAATA+TCGACATC NW_022994971.1 30287 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1560:16206:24392_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18140 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1577:23285:35618_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18122 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1620:6442:2879_1:N:0:CTCGAATA+TCGACATC NW_022994939.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1631:29866:25160_1:N:0:CTCGAATA+TCGACATC NW_022994948.1 858070 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1633:19352:34100_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1634:20980:3004_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18140 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1643:31919:1595_1:N:0:CTCGAATA+TCGACATC NW_022994934.1 1 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1651:29649:4366_1:N:0:CTCGAATA+TCGACATC NW_022994997.1 1 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2105:6307:27258_1:N:0:CTCGAATA+TCGACATC NW_022994909.1 80225 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2107:3405:34037_1:N:0:CTCGAATA+TCGACATC NW_022994905.1 1 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2125:1958:13463_1:N:0:CTCGAATA+TCGACATC NW_022994832.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2130:1714:36839_1:N:0:CTCGAATA+TCGACATC NW_022994973.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2131:2031:2347_1:N:0:CTCGAATA+TCGACATC NW_022994973.1 2 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2146:28890:18490_1:N:0:CTCGAATA+TCGACATC NW_022994924.1 127753 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2151:27859:1642_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 2 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2162:8495:13792_1:N:0:CTCGAATA+TCGACATC NW_022994970.1 1 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2170:12662:6230_1:N:0:CTCGAATA+TCGACATC NW_022994924.1 127747 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2207:16016:30326_1:N:0:CTCGAATA+TCGACATC NW_022994974.1 36470 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2207:18511:34710_1:N:0:CTCGAATA+TCGACATC NW_022994974.1 36471 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2216:19190:21950_1:N:0:CTCGAATA+TCGACATC NW_022994989.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2216:15890:27038_1:N:0:CTCGAATA+TCGACATC NW_022994989.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2219:13801:4006_1:N:0:CTCGAATA+TCGACATC NC_047563.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2224:7265:7153_1:N:0:CTCGAATA+TCGACATC NW_022994902.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2225:20582:2816_1:N:0:CTCGAATA+TCGACATC NW_022994916.1 2 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2235:2175:3411_1:N:0:CTCGAATA+TCGACATC NW_022994925.1 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2244:18132:35712_1:N:0:CTCGAATA+TCGACATC NW_022994875.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2254:5999:12289_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2257:13096:29653_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2257:11677:30264_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2257:11614:30342_1:N:0:CTCGAATA+TCGACATC NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2258:31828:9737_1:N:0:CTCGAATA+TCGACATC NW_022994905.1 3 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2276:10438:30029_1:N:0:CTCGAATA+TCGACATC NW_022994786.1 2 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2303:3522:31704_1:N:0:CTCGAATA+TCGACATC NW_022994875.1 2 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2317:5656:9283_1:N:0:CTCGAATA+TCGACATC NW_022994917.1 1 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2347:12852:30389_1:N:0:CTCGAATA+TCGACATC NW_022994778.1 761867 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:1371:11537_1:N:0:CTCGAATA+TCGACATC NW_022994793.1 65970 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:1217:31720_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2368:31467:23265_1:N:0:CTCGAATA+TCGACATC NW_022994964.1 245875 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2372:31620:3521_1:N:0:CTCGAATA+TCGACATC NW_022994935.1 43754 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2375:28944:4836_1:N:0:CTCGAATA+TCGACATC NW_022994993.1 225128 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2377:5312:7842_1:N:0:CTCGAATA+TCGACATC NW_022994924.1 127735 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2406:4209:35493_1:N:0:CTCGAATA+TCGACATC NW_022994906.1 24078 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2427:26946:22701_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18130 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2447:6433:27070_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2449:24523:6480_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18126 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:19271:6965_1:N:0:CTCGAATA+TCGACATC NW_022994925.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2463:24822:31735_1:N:0:CTCGAATA+TCGACATC NW_022994792.1 66677 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2464:21287:3255_1:N:0:CTCGAATA+TCGACATC NW_022994902.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2467:20835:3975_1:N:0:CTCGAATA+TCGACATC NC_001276.1 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2474:16333:31438_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18138 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2550:32796:7686_1:N:0:CTCGAATA+TCGACATC NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2551:9588:26804_1:N:0:CTCGAATA+TCGACATC NW_022994904.1 192205 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2555:13105:5149_1:N:0:CTCGAATA+TCGACATC NW_022994933.1 2 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2621:30481:11631_1:N:0:CTCGAATA+TCGACATC NW_022994822.1 614022 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2621:27407:17926_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18111 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2646:8422:14606_1:N:0:CTCGAATA+TCGACATC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2647:23213:15421_1:N:0:CTCGAATA+TCGACATC NW_022994939.1 324551 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2650:2537:6261_1:N:0:CTCGAATA+TCGACATC NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2656:18620:14074_1:N:0:CTCGAATA+TCGACATC NW_022994930.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2657:26992:30013_1:N:0:CTCGAATA+TCGACATC NW_022994934.1 1 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far 76522716 reads; of these: 76522716 (100.00%) were paired; of these: 56179829 (73.42%) aligned concordantly 0 times 9274621 (12.12%) aligned concordantly exactly 1 time 11068266 (14.46%) aligned concordantly >1 times 26.58% overall alignment rate 76522716 reads; of these: 76522716 (100.00%) were paired; of these: 56130549 (73.35%) aligned concordantly 0 times 9293359 (12.14%) aligned concordantly exactly 1 time 11098808 (14.50%) aligned concordantly >1 times 26.65% overall alignment rate 76522716 reads; of these: 76522716 (100.0076522716% reads; of these:) were paired; of these: 7652271656172031 ( (73.41%) aligned concordantly 0 times 9267439100.00 (%12.11) were paired; of these:% ) aligned concordantly exactly 1 time 56140900 (1108324673.37 (%14.48) aligned concordantly 0 times% ) aligned concordantly >1 times 929740226.59 (%12.15 overall alignment rate% ) aligned concordantly exactly 1 time 11084414 (14.49%) aligned concordantly >1 times 26.63% overall alignment rate Processed 76522716 sequences in total Successfully deleted the temporary files zr3534_1_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_1_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_1_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_1_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 76522716 Number of paired-end alignments with a unique best hit: 47127724 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 17253197 Sequence pairs did not map uniquely: 12141795 Sequence pairs which were discarded because genomic sequence could not be extracted: 96 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11765055 ((converted) top strand) GA/CT/CT: 11788130 (complementary to (converted) top strand) GA/CT/GA: 11797392 (complementary to (converted) bottom strand) CT/GA/GA: 11777051 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1636781777 Total methylated C's in CpG context: 22358259 Total methylated C's in CHG context: 1394261 Total methylated C's in CHH context: 5914275 Total methylated C's in Unknown context: 52616 Total unmethylated C's in CpG context: 191433820 Total unmethylated C's in CHG context: 285827469 Total unmethylated C's in CHH context: 1129853693 Total unmethylated C's in Unknown context: 3992972 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 15h 43m 5s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_2_R1.fastp-trim.20201202.fq.gz to zr3534_2_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R1.fastp-trim.20201202.fq.gz to zr3534_2_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R1.fastp-trim.20201202.fq.gz (75413899 sequences in total) Writing a C -> T converted version of the input file zr3534_2_R2.fastp-trim.20201202.fq.gz to zr3534_2_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R2.fastp-trim.20201202.fq.gz to zr3534_2_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R2.fastp-trim.20201202.fq.gz (75413899 sequences in total) Input files are zr3534_2_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_2_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_2_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ATAAAATATTAATAAATTAATTAAATAATTTTAAAATTAATAAATAATAAAAATTTAAAATAATATAATATATTTTATTTTAATTAAAATATAATAATAATTTTTAAAATATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTATTTTTATTATTTAAATATATTAAAAAATTTAAAAAATTTTTATTATTAATAATTAATTTATTATTTTATTATAAAATTTTATTTTAATAAAATATATTAATAAAATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_2_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 99 NC_047562.1_GA_converted 34078973 42 115M = 34079087 228 ACAAAATATTAACAAATTAACCAAACAACTTTAAAATCAACAAACAACAAAAATTTAAAATAATACAACATATTTTACTTCAATCAAAATATAATAACAATCCTCAAAATACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:0 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 147 NC_047562.1_GA_converted 34079087 42 114M = 34078973 -228 ACTAAATTTCATCAATATATTCCATCAAAATAAAATTTTATAACAAAACAACAAATTAATTACCAACAATAAAAATTCTCTAAATTCCTTAATATATTTAAATAATAAAAACAA FFFFFFFF:FF:FFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:114 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_2_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ACAAAATATTAACAAATTAACCAAACAACTTTAAAATCAACAAACAACAAAAATTTAAAATAATACAACATATTTTACTTCAATCAAAATATAATAACAATCCTCAAAATACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTGTTTTTATTATTTAAATATATTAAGGAATTTAGAGAATTTTTATTGTTGGTAATTAATTTGTTGTTTTGTTATAAAATTTTATTTTGATGGAATATATTGATGAAATTTAGT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_2_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ATAAAATATTAATAAATTAATTAAATAATTTTAAAATTAATAAATAATAAAAATTTAAAATAATATAATATATTTTATTTTAATTAAAATATAATAATAATTTTTAAAATATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTATTTTTATTATTTAAATATATTAAAAAATTTAAAAAATTTTTATTATTAATAATTAATTTATTATTTTATTATAAAATTTTATTTTAATAAAATATATTAATAAAATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1106:32208:17221_1:N:0:GATCGTCG+ACATATCC NW_022994929.1 46764 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1115:29875:31751_1:N:0:GATCGTCG+ACATATCC NW_022994804.1 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1125:27859:35086_1:N:0:GATCGTCG+ACATATCC NW_022994828.1 316058 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1141:19343:1986_1:N:0:GATCGTCG+ACATATCC NW_022994814.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1150:31810:23077_1:N:0:GATCGTCG+ACATATCC NW_022994817.1 2142 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1205:22923:23343_1:N:0:GATCGTCG+ACATATCC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1207:13539:36965_1:N:0:GATCGTCG+ACATATCC NW_022994810.1 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1219:30364:35227_1:N:0:GATCGTCG+ACATATCC NW_022994919.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1230:26051:16799_1:N:0:GATCGTCG+ACATATCC NW_022994916.1 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1236:14751:4993_1:N:0:GATCGTCG+ACATATCC NW_022994925.1 61439 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1240:10547:21042_1:N:0:GATCGTCG+ACATATCC NW_022994881.1 520542 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1243:15157:5165_1:N:0:GATCGTCG+ACATATCC NW_022994777.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1244:32741:25160_1:N:0:GATCGTCG+ACATATCC NC_001276.1 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1249:8006:10598_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18134 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1251:17409:34961_1:N:0:GATCGTCG+ACATATCC NW_022994925.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1254:17644:34428_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1255:6605:8296_1:N:0:GATCGTCG+ACATATCC NW_022994951.1 3 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1261:26585:5165_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1266:4463:30545_1:N:0:GATCGTCG+ACATATCC NW_022994940.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1273:11650:15405_1:N:0:GATCGTCG+ACATATCC NW_022994832.1 513204 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1273:7066:15702_1:N:0:GATCGTCG+ACATATCC NW_022994832.1 513204 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1312:13765:13683_1:N:0:GATCGTCG+ACATATCC NW_022994898.1 63861 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1337:13874:6073_1:N:0:GATCGTCG+ACATATCC NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1340:13440:26866_1:N:0:GATCGTCG+ACATATCC NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1340:10899:33364_1:N:0:GATCGTCG+ACATATCC NW_022994966.1 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1343:26124:6151_1:N:0:GATCGTCG+ACATATCC NW_022994946.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1346:26494:5228_1:N:0:GATCCTCG+ACATATCC NC_001276.1 18126 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1439:9227:20102_1:N:0:GATCGTCG+ACATATCC NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1447:25762:31046_1:N:0:GATCGTCG+ACATATCC NW_022994850.1 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1457:32154:33129_1:N:0:GATCGTCG+ACATATCC NW_022994911.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1461:7970:7654_1:N:0:GATCGTCG+ACATATCC NW_022994777.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1462:5430:4977_1:N:0:GATCGTCG+ACATATCC NW_022994981.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1466:3983:22701_1:N:0:GATCGTCG+ACCTATCC NW_022994946.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1470:18521:1689_1:N:0:GATCGTCG+ACATATCC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1471:6027:4038_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18126 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1505:11297:17425_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1507:25789:7420_1:N:0:GATCGTCG+ACATATCC NW_022994950.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1508:16197:12759_1:N:0:GATCGTCG+ACATATCC NW_022994822.1 614058 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1516:3866:21590_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1519:9995:4460_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1519:9896:4633_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18116 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1529:14895:19899_1:N:0:GATCGTCG+ACATATCC NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1529:17526:21574_1:N:0:GATCGTCG+ACATATCC NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1532:16604:13964_1:N:0:GATCGTCG+ACATATCC NW_022994905.1 1 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1555:1615:22514_1:N:0:GATCGTCG+ACATATCC NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1558:31186:20400_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18126 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1566:20862:26850_1:N:0:GATCGTCG+ACATATCC NC_001276.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1573:2049:24298_1:N:0:GATCGTCG+ACATATCC NW_022994911.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1574:22489:21433_1:N:0:GATCGTCG+ACATATCC NW_022994965.1 30584 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1574:21721:24392_1:N:0:GATCGTCG+ACATATCC NW_022994965.1 30584 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1624:1163:16939_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18116 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1633:29640:22075_1:N:0:GATCGTCG+ACATATCC NW_022994819.1 2 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1657:6858:2597_1:N:0:GATCGTCG+ACATATCC NW_022994917.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1674:10845:14544_1:N:0:GATCGTCG+ACATATCC NW_022994936.1 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2113:15537:21512_1:N:0:GATCGTCG+ACATATCC NC_001276.1 3 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2144:1597:22106_1:N:0:GATCGTCG+ACATATCC NW_022994902.1 2 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2155:19750:27618_1:N:0:GATCGTCG+ACATATCC NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2158:16767:19539_1:N:0:GATCGTCG+ACATATCC NW_022994965.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2164:6334:31438_1:N:0:GATCGTCG+ACATATCC NW_022994988.1 28370 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2203:23330:30373_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2203:23909:30373_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18110 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2211:29288:19930_1:N:0:GATCGTCG+ACATATCC NW_022994898.1 63859 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2228:31684:1376_1:N:0:GATCGTCG+ACATATCC NW_022994964.1 245873 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2236:8241:27320_1:N:0:GATCGTCG+ACATATCC NW_022994792.1 66676 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2244:25030:31344_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2245:28709:31109_1:N:0:GATCGTCG+ACTTATCC NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2245:28926:33051_1:N:0:GATCGTCG+ACATATCC NW_022994911.1 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2256:17192:34366_1:N:0:GATCGTCG+ACATATCC NW_022994930.1 3 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2306:27751:6558_1:N:0:GATCGTCG+ACATATCC NW_022994902.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2306:27615:9799_1:N:0:GATCGTCG+ACATATCC NW_022994902.1 3 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2326:1461:29888_1:N:0:GATCGTCG+ACATATCC NW_022994985.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2329:1940:25582_1:N:0:GATCGTCG+ACATATCC NW_022994962.1 1 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2335:18756:20541_1:N:0:GATCGTCG+ACATATCC NW_022994930.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2336:13268:17644_1:N:0:GATCGTCG+ACATATCC NW_022994933.1 29878 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2337:28854:21339_1:N:0:GATCGTCG+ACATATCC NW_022994951.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2340:13810:31673_1:N:0:GATCGTCG+ACATATCC NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2341:12002:6433_1:N:0:GATCGTCG+ACATATCC NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2341:12057:6433_1:N:0:GATCGTCG+ACATATCC NW_022994786.1 2 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2350:15130:26694_1:N:0:GATCGTCG+ACATATCC NW_022994985.1 189982 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:31801:33019_1:N:0:GATCGTCG+ACATATCC NW_022994987.1 316348 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2402:2320:33317_1:N:0:GATCGTCG+ACATATCC NW_022994925.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2404:16911:28432_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18116 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2408:1579:30029_1:N:0:GATCGTCG+ACATATCC NW_022994952.1 218888 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2415:3468:35900_1:N:0:GATCGTCG+ACATATCC NW_022994917.1 1 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:4978:1658_1:N:0:GATCGTCG+ACATATCC NW_022994777.1 2 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2476:28718:27649_1:N:0:GATCGTCG+ACATATCC NW_022994926.1 1 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:27353:15233_1:N:0:GATCGTCG+ACATATCC NW_022994929.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:6216:25567_1:N:0:GATCGTCG+ACATATCC NW_022994898.1 63869 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2503:11433:27117_1:N:0:GATCGTCG+ACATATCC NW_022994936.1 296929 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2505:20654:7701_1:N:0:GATCGTCG+ACATATCC NC_001276.1 1 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2515:32027:26459_1:N:0:GATCGTCG+ACATATCC NW_022994970.1 1 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2530:21585:16078_1:N:0:GATCGTCG+ACATAACC NW_022994817.1 2147 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2531:10104:8061_1:N:0:GATCGTCG+ACATATCC NW_022994911.1 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2543:24994:22545_1:N:0:GATCGTCG+ACATATCC NW_022994893.1 1 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2618:19443:4413_1:N:0:GATCGTCG+ACATATCC NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2620:31548:17206_1:N:0:GATCGTCG+ACATATCC NW_022994804.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2620:30246:16485_1:N:0:GATCGTCG+ACATATCC NW_022994804.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2622:16269:13228_1:N:0:GATCGTCG+ACATATCC NW_022994846.1 330784 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2622:23692:36072_1:N:0:GATCGTCG+ACATATCC NW_022994989.1 2 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2629:19407:27430_1:N:0:GATCGTCG+ACATATCC NC_001276.1 18109 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2643:25717:25614_1:N:0:GATCGTCG+ACATATCC NW_022994893.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2643:25644:28025_1:N:0:GATCGTCG+ACATATCC NW_022994893.1 1 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far 75413899 reads; of these: 75413899 (100.00%) were paired; of these: 55218157 (73.22%) aligned concordantly 0 times 9106846 (12.08%) aligned concordantly exactly 1 time 11088896 (14.70%) aligned concordantly >1 times 26.78% overall alignment rate 75413899 reads; of these: 75413899 (100.00%) were paired; of these: 55313503 (73.35%) aligned concordantly 0 times 9056413 (12.01%) aligned concordantly exactly 1 time 11043983 (14.64%) aligned concordantly >1 times 26.65% overall alignment rate 75413899 reads; of these: 75413899 (100.00%) were paired; of these: 55236218 (73.24%) aligned concordantly 0 times 9099948 (12.07%) aligned concordantly exactly 1 time 11077733 (14.69%) aligned concordantly >1 times 26.76% overall alignment rate 75413899 reads; of these: 75413899 (100.00%) were paired; of these: 55336376 (73.38%) aligned concordantly 0 times 9052995 (12.00%) aligned concordantly exactly 1 time 11024528 (14.62%) aligned concordantly >1 times 26.62% overall alignment rate Processed 75413899 sequences in total Successfully deleted the temporary files zr3534_2_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_2_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_2_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_2_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 75413899 Number of paired-end alignments with a unique best hit: 46140925 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 17015547 Sequence pairs did not map uniquely: 12257427 Sequence pairs which were discarded because genomic sequence could not be extracted: 102 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11482323 ((converted) top strand) GA/CT/CT: 11541123 (complementary to (converted) top strand) GA/CT/GA: 11582832 (complementary to (converted) bottom strand) CT/GA/GA: 11534545 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1612045578 Total methylated C's in CpG context: 21945879 Total methylated C's in CHG context: 1370392 Total methylated C's in CHH context: 5818112 Total methylated C's in Unknown context: 53662 Total unmethylated C's in CpG context: 190060088 Total unmethylated C's in CHG context: 281860222 Total unmethylated C's in CHH context: 1110990885 Total unmethylated C's in Unknown context: 3919471 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 15h 40m 28s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_3_R1.fastp-trim.20201202.fq.gz to zr3534_3_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R1.fastp-trim.20201202.fq.gz to zr3534_3_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R1.fastp-trim.20201202.fq.gz (78091157 sequences in total) Writing a C -> T converted version of the input file zr3534_3_R2.fastp-trim.20201202.fq.gz to zr3534_3_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R2.fastp-trim.20201202.fq.gz to zr3534_3_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R2.fastp-trim.20201202.fq.gz (78091157 sequences in total) Input files are zr3534_3_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_3_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_3_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 TATATAATTAATTTTTATTTTTTAATATATATTATAATTTTTATTAATATTATAATTAAAAAAAATTATTATTAATAAAAATTAAAAAATTATAAATATTAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 ATTTATAATTTTTTAATTTTTATTAATAATAATTTTTTTTAATTATAATATTAATAAAAATTATAATATATATTAAAAAATAAAAATTAATTATATAATTATTATAA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_3_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 CATACAATTAACTTTTATCTTTTAATATATACCATAACTTCTATTAACACTATAATCAAAAAAAACTACTACCAACAAAAATTAAAAAACTACAAACACTAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 GTTTGTAGTTTTTTAATTTTTGTTGGTAGTAGTTTTTTTTGATTATAGTGTTAATAGAAGTTATGGTATATATTAAAAGATAAAAGTTAATTGTATGATTGTTGTGA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_3_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 CATACAATTAACTTTTATCTTTTAATATATACCATAACTTCTATTAACACTATAATCAAAAAAAACTACTACCAACAAAAATTAAAAAACTACAAACACTAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 GTTTGTAGTTTTTTAATTTTTGTTGGTAGTAGTTTTTTTTGATTATAGTGTTAATAGAAGTTATGGTATATATTAAAAGATAAAAGTTAATTGTATGATTGTTGTGA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_3_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 TATATAATTAATTTTTATTTTTTAATATATATTATAATTTTTATTAATATTATAATTAAAAAAAATTATTATTAATAAAAATTAAAAAATTATAAATATTAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 ATTTATAATTTTTTAATTTTTATTAATAATAATTTTTTTTAATTATAATATTAATAAAAATTATAATATATATTAAAAAATAAAAATTAATTATATAATTATTATAA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1105:25021:2675_1:N:0:TATCCGAG+CTTATTGG NW_022994940.1 2 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1124:17011:10347_1:N:0:TATCCGAG+CTTATTGG NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1124:16188:20760_1:N:0:TATCCGAG+CTTATTGG NW_022994911.1 90158 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1133:20546:17942_1:N:0:TATCCGAG+CTTATTGG NW_022994987.1 316387 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1174:17978:3129_1:N:0:TATCCGAG+CTTATTGG NW_022994946.1 333522 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1174:19895:19100_1:N:0:TATCCGAG+CTTATTGG NW_022994777.1 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1206:29035:9502_1:N:0:TATCCGAG+CTTATTGG NW_022994968.1 91891 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1222:20455:31594_1:N:0:TATCCGAG+CTTATTGG NW_022994978.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1228:25970:1407_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1238:19081:5102_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 172701 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1240:14136:23813_1:N:0:TATCCGAG+CTTATTGG NW_022994989.1 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1253:19488:30452_1:N:0:TATCCGAG+CTTATTGG NW_022994957.1 201032 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1258:17653:15468_1:N:0:TATCCGAG+CTTATTGG NW_022994804.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1260:28293:33207_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1263:12328:4617_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1271:18656:13636_1:N:0:TATCCGAG+CTTATTGG NW_022994985.1 189982 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1314:10999:26083_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1314:10954:26443_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1314:10456:28494_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1321:6795:4210_1:N:0:TATCCGAG+CTTATTGG NW_022994916.1 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1337:4987:16611_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1337:30418:23860_1:N:0:TATCCGAG+CTTATTGG NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1340:26006:16658_1:N:0:TATCCGAG+CTTATTGG NW_022994966.1 1 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1424:6189:21637_1:N:0:TATCCGAG+CTTATTGG NW_022994946.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1435:23276:2440_1:N:0:TATCCGAG+CTTATTGG NW_022994820.1 658256 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1439:29432:26506_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18109 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1441:4996:7263_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1441:7943:9486_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1445:31638:3615_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1468:31846:20760_1:N:0:TATCCGAG+CTTATTGG NW_022994946.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1501:4200:14559_1:N:0:TATCCGAG+CTTATTGG NW_022994936.1 296937 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1504:23972:12007_1:N:0:TATCCGAG+CTTATTGG NW_022994971.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1518:2663:24706_1:N:0:TATCCGAG+CTTATTGG NW_022994817.1 2152 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1526:11261:10535_1:N:0:TATCCGAG+CTTATTGC NW_022994970.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1528:17155:16235_1:N:0:TATCCGAG+CTTATTGG NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1530:31277:4773_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18126 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1540:14154:5181_1:N:0:TATCCGAG+CTTATTGG NW_022994924.1 127733 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1542:19913:30906_1:N:0:TATCCGAG+CTTATTGG NW_022994905.1 1 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1563:31702:35947_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18110 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1603:2257:3959_1:N:0:TATCCGAG+CTTATTGG NW_022994975.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1603:1705:6668_1:N:0:TATCCGAG+CTTATTGG NW_022994975.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1612:2293:32142_1:N:0:TATCCGAG+CTTATTGG NW_022994924.1 127737 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1612:2691:32643_1:N:0:TATCCGAG+CTTATTGG NW_022994924.1 127737 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1647:29234:28729_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1648:4282:33677_1:N:0:TATCCGAG+CTTATTGG NW_022994906.1 24085 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1670:24939:27430_1:N:0:TATCCGAG+CTTATTGG NW_022994920.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1673:5629:16501_1:N:0:TATCCGAG+CTTATTGG NW_022994952.1 218896 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2131:24370:23124_1:N:0:TATCCGAG+CTTATTGG NW_022994808.1 3 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2141:17065:12571_1:N:0:TATCCGAG+CTTATTGG NW_022994988.1 28363 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2152:31367:19711_1:N:0:TATCCGAG+CTTATTGG NW_022994951.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2156:6198:28541_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2157:12075:22748_1:N:0:TATCCGAG+CTTATTGG NW_022994835.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2171:3667:2206_1:N:0:TATCCGAG+CTTATTGG NW_022994940.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2171:3477:4977_1:N:0:TATCCGAG+CTTATTGG NW_022994940.1 2 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2206:25003:35243_1:N:0:TATCCGAG+CTTATTGG NW_022994934.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2215:30960:26459_1:N:0:TATCCGAG+CTTATTGG NW_022994962.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2226:12943:12790_1:N:0:TATCCGAG+CTTATTGG NW_022994917.1 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2231:8829:30217_1:N:0:TATCCGAG+CTTATTGG NW_022994994.1 1 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2242:19009:4601_1:N:0:TATCCGAG+CTTATTGG NW_022994978.1 113587 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2277:26738:19617_1:N:0:TATCCGAG+CTTATTGG NW_022994997.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2277:24080:23343_1:N:0:TATCCGAG+CTTATTGG NW_022994997.1 2 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2323:12762:7686_1:N:0:TATCCGAG+CTTATTGG NW_022994957.1 201085 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2354:9362:23657_1:N:0:TATCCGAG+CTTATTGG NW_022994916.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2354:9272:24283_1:N:0:TATCCGAG+CTTATTGG NW_022994916.1 3 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2360:5837:32706_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 172712 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2409:29631:18082_1:N:0:TATCCGAG+CTTATTGG NW_022994952.1 218897 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2409:29577:18114_1:N:0:TATCCGAG+CTTATTGG NW_022994952.1 218897 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2409:32642:18975_1:N:0:TATCCGAG+CTTATTGG NW_022994952.1 218897 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2440:12744:19492_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 1 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2455:29767:20509_1:N:0:TATCCGAG+CTTATTGG NW_022994915.1 2 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2471:29387:15781_1:N:0:TATCCGAG+CTTATTGG NW_022994946.1 333522 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2472:22381:12665_1:N:0:TATCCGAG+CTTATTGG NW_022994898.1 63859 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2513:32895:9361_1:N:0:TATCCGAG+ATTATTGG NW_022994940.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2513:21649:14622_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2513:20980:15530_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2523:29342:1955_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18126 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2541:26015:17801_1:N:0:TATCCGAG+CTTATTGG NW_022994797.1 60084 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2553:3278:7921_1:N:0:TATCCGAG+CTTATTGG NW_022994978.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2557:24017:5885_1:N:0:TATCCGAG+CTTATTGG NW_022994935.1 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2561:19361:24377_1:N:0:TATCCGAG+CTTATTGG NW_022994893.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2563:21612:25113_1:N:0:TATCCGAG+CTTATTGG NW_022994804.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2566:25256:14669_1:N:0:TATCCGAG+CTTATTGG NW_022994951.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2570:25789:22576_1:N:0:TATCCGAG+CTTATTGG NW_022994957.1 201085 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2570:23936:25379_1:N:0:TATCCGAG+CTTATTGG NW_022994957.1 201085 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2601:24677:8155_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 2 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2614:27534:8343_1:N:0:TATCCGAG+CTTATTGG NW_022994958.1 2 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2626:11297:19366_1:N:0:TATCCGAG+CTTATTGG NW_022994908.1 34607 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2637:4237:9236_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18140 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2650:11686:7827_1:N:0:TATCCGAG+CTTATTGG NW_022994940.1 1 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2653:23267:27226_1:N:0:TATCCGAG+CTTATTGG NW_022994971.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2655:9281:12148_1:N:0:TATCCGAG+CTTATTGG NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2659:11496:30671_1:N:0:TATCCGAG+CTTATTGG NW_022994925.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2664:21477:7059_1:N:0:TATCCGAG+CTTATTGG NW_022994793.1 66010 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2670:22263:28745_1:N:0:TATCCGAG+CTTATTGG NW_022994920.1 2 Processed 78000000 sequence pairs so far 78091157 reads; of these: 78091157 (100.00%) were paired; of these: 57539322 (73.68%) aligned concordantly 0 times 9340984 (11.96%) aligned concordantly exactly 1 time 11210851 (14.36%) aligned concordantly >1 times 26.32% overall alignment rate 78091157 reads; of these: 78091157 (100.00%) were paired; of these: 57617593 (73.78%) aligned concordantly 0 times 9319771 (11.93%) aligned concordantly exactly 1 time 11153793 (14.28%) aligned concordantly >1 times 26.22% overall alignment rate 78091157 reads; of these: 78091157 (100.00%) were paired; of these: 57509582 (73.64%) aligned concordantly 0 times 9355714 (11.98%) aligned concordantly exactly 1 time 11225861 (14.38%) aligned concordantly >1 times 26.36% overall alignment rate 78091157 reads; of these: 78091157 (100.00%) were paired; of these: 57594554 (73.75%) aligned concordantly 0 times 9326455 (11.94%) aligned concordantly exactly 1 time 11170148 (14.30%) aligned concordantly >1 times 26.25% overall alignment rate Processed 78091157 sequences in total Successfully deleted the temporary files zr3534_3_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_3_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_3_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_3_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 78091157 Number of paired-end alignments with a unique best hit: 47623705 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 18311792 Sequence pairs did not map uniquely: 12155660 Sequence pairs which were discarded because genomic sequence could not be extracted: 94 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11910708 ((converted) top strand) GA/CT/CT: 11863283 (complementary to (converted) top strand) GA/CT/GA: 11897437 (complementary to (converted) bottom strand) CT/GA/GA: 11952183 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1670693519 Total methylated C's in CpG context: 25533290 Total methylated C's in CHG context: 1462648 Total methylated C's in CHH context: 6171814 Total methylated C's in Unknown context: 61366 Total unmethylated C's in CpG context: 191641924 Total unmethylated C's in CHG context: 289598207 Total unmethylated C's in CHH context: 1156285636 Total unmethylated C's in Unknown context: 4126149 C methylated in CpG context: 11.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 16h 14m 18s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_4_R1.fastp-trim.20201202.fq.gz to zr3534_4_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R1.fastp-trim.20201202.fq.gz to zr3534_4_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R1.fastp-trim.20201202.fq.gz (74728031 sequences in total) Writing a C -> T converted version of the input file zr3534_4_R2.fastp-trim.20201202.fq.gz to zr3534_4_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R2.fastp-trim.20201202.fq.gz to zr3534_4_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R2.fastp-trim.20201202.fq.gz (74728031 sequences in total) Input files are zr3534_4_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_4_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_4_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAGAATGAAGTTTAATTAAATGTATATATGAGAATTATTAAAAGGTTTGTATGGGTTATAGAAATTGTTAAGGATTGTTTATTTTTTGTAAGATTTTTTTATTTTTTAGGTGAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATCATCTTTAAATTCTCCCTAAAAATAACTTAAAAATACAAAACAAAAAAATCAAAAAATCTTTCACCTAAAAAATAAAAAAATCTTACAAAAAATAAACAATCCTTAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_4_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATTTAATTAAATATATATATAAAAATTATTAAAAAATTTATATAAATTATAAAAATTATTAAAAATTATTTATTTTTTATAAAATTTTTTTATTTTTTAAATAAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATTATTTTTAAATTTTTTTTAAAAATAATTTAAAAATATAAAATAAAAAAATTAAAAAATTTTTTATTTAAAAAATAAAAAAATTTTATAAAAAATAAATAATTTTTAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_4_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATTTAATTAAATATATATATAAAAATTATTAAAAAATTTATATAAATTATAAAAATTATTAAAAATTATTTATTTTTTATAAAATTTTTTTATTTTTTAAATAAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATTATTTTTAAATTTTTTTTAAAAATAATTTAAAAATATAAAATAAAAAAATTAAAAAATTTTTTATTTAAAAAATAAAAAAATTTTATAAAAAATAAATAATTTTTAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_4_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAGAATGAAGTTTAATTAAATGTATATATGAGAATTATTAAAAGGTTTGTATGGGTTATAGAAATTGTTAAGGATTGTTTATTTTTTGTAAGATTTTTTTATTTTTTAGGTGAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATCATCTTTAAATTCTCCCTAAAAATAACTTAAAAATACAAAACAAAAAAATCAAAAAATCTTTCACCTAAAAAATAAAAAAATCTTACAAAAAATAAACAATCCTTAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1101:27272:31219_1:N:0:CGCTGTCT+GGTGAGTA NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1112:30364:28776_1:N:0:CGCTGTCT+GGTGAGTA NW_022994925.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1112:30888:30906_1:N:0:CGCTGTCT+GGTGAGTA NW_022994925.1 1 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1132:22978:10848_1:N:0:CGCTGTCT+GGTGAGTA NW_022994960.1 137397 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1132:16731:27899_1:N:0:CGCTGTCT+GGTGAGTA NW_022994966.1 514693 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1137:31485:22200_1:N:0:CGCTGTCT+GGTGAGTA NW_022994911.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1137:13322:31140_1:N:0:CGCTGTCT+GGTGAGTA NW_022994898.1 63874 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1144:13268:21934_1:N:0:CGCTGTCT+GGTGAGTA NW_022994953.1 45716 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1166:24261:7560_1:N:0:CGCTGTCT+GGTGAGTA NW_022994804.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1202:15212:20040_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1203:13621:10989_1:N:0:CGCTGTCT+GGTGAGTA NW_022994812.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1205:21043:31360_1:N:0:CGCTGTCT+GGTGAGTA NW_022994881.1 520519 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1244:8965:22842_1:N:0:CGCTGTCT+GGTGAGTA NW_022994972.1 189631 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1249:32172:36793_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1252:26106:5494_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1252:22553:8954_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1256:2763:26976_1:N:0:CGCTGTCT+GGTGAGTA NW_022994974.1 36491 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1264:22146:31986_1:N:0:CGCTGTCT+GGTGAGTA NW_022994997.1 297105 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1268:16098:32471_1:N:0:CGCTGTCT+GGTGAGTA NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1268:32913:33505_1:N:0:CGCTGTCT+GGTGAGTA NW_022994951.1 2 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1309:10682:35180_1:N:0:CGCTGTCT+GGTGAGTA NW_022994972.1 189639 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1315:16423:16344_1:N:0:CGCTGTCT+GGTGAGTA NW_022994906.1 24090 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1328:13584:9142_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18126 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1334:2456:35963_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18116 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1347:23601:3443_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18111 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1357:19804:5447_1:N:0:CGCTGTCT+GGTGAGTA NW_022994944.1 261202 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1365:21269:4695_1:N:0:CGCTGTCT+GGTGAGTA NW_022994962.1 2 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1510:9616:9721_1:N:0:CGCTGTCT+GGTGAGTA NW_022994846.1 1 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1528:13675:1564_1:N:0:CGCTGTCT+GGTGAGTA NW_022994968.1 91883 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1528:22200:29825_1:N:0:CGCTGTCT+GGTGAGTA NW_022994958.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1534:15637:11882_1:N:0:CGCTGTCT+GGTGAGTA NW_022994960.1 137416 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1543:7057:3317_1:N:0:CGCTGTCT+GGTGAGTA NW_022994927.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1546:21495:19053_1:N:0:CGCTGTCT+GGTGAGTA NW_022994904.1 192198 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1547:13150:10394_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1548:5132:8782_1:N:0:CGCTGTCT+GGTGAGTA NW_022994965.1 30631 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1551:17680:27759_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1560:21052:10708_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1561:11957:34350_1:N:0:CGCTGTCT+GGTGAGTA NW_022994989.1 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1562:4661:35869_1:N:0:CGCTGTCT+GGTGAGTA NW_022994993.1 225126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1565:21486:28369_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1577:5746:15859_1:N:0:CGCTGTCT+GGTGAGTA NW_022994960.1 137386 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1615:24171:26819_1:N:0:CGCTGTCT+GGTGAGTA NW_022994960.1 137416 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1638:2320:21418_1:N:0:CGCTGTCT+GGTGAGTA NW_022994939.1 324548 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1653:5710:1548_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18117 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1658:17698:21277_1:N:0:CGCTGTCT+GGTGAGTA NW_022994903.1 3 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1671:15049:9392_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18111 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2101:30147:25457_1:N:0:CGCTGTCT+GGTGAGTA NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2106:21884:5134_1:N:0:CGCTGTCT+GGTGAGTA NW_022994975.1 74070 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2106:21576:5196_1:N:0:CGCTGTCT+GGTGAGTA NW_022994975.1 74070 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2106:23276:7075_1:N:0:CGCTGTCT+GGTGAGTA NW_022994975.1 74070 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2108:28339:18912_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2117:18222:36839_1:N:0:CGCTGTCT+GGTGAGTA NW_022994816.1 1 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2124:25681:17127_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18117 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2133:3757:9220_1:N:0:CGCTGTCT+GGTGAGTA NW_022994951.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2133:9878:11929_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18110 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2145:9417:1235_1:N:0:CGCTGTCT+GGTGAGTA NW_022994953.1 45716 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:11812:33035_1:N:0:CGCTGTCT+GGTGAGTA NW_022994911.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2169:17065:2988_1:N:0:CGCTGTCT+GGTGAGTA NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2171:11632:33254_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18142 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2215:23131:4570_1:N:0:CGCTGTCT+GGTGAGTA NW_022994790.1 1 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2221:21106:18944_1:N:0:CGCTGTCT+GGTGAGTA NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2222:28908:5932_1:N:0:CGCTGTCT+GGTGAGTA NW_022994921.1 323436 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2257:19443:16438_1:N:0:CGCTGTCT+GGTGAGTA NW_022994974.1 3 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2269:24062:22216_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18187 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2273:10031:22968_1:N:0:CGCTGTCT+GGTGAGTA NW_022994900.1 158491 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2301:5376:5760_1:N:0:CGCTGTCT+GGTGAGTA NW_022994981.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2302:10682:6872_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2307:13729:24831_1:N:0:CGCTGTCT+GGTGAGTA NW_022994810.1 3 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2351:11623:12383_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2359:30445:4085_1:N:0:CGCTGTCT+GGTGAGTA NW_022994874.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2361:6686:31892_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18130 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2365:27163:35634_1:N:0:CGCTGTCT+GGTGAGTA NW_022994810.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2366:27877:7905_1:N:0:CGCTGTCT+GGTGAGTA NW_022994810.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:24406:14325_1:N:0:CGCTGTCT+GGTGAGTA NW_022994972.1 189639 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2371:18448:6292_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18122 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2376:20220:18411_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2410:22661:17033_1:N:0:CGCTGTCT+GGTGAGTA NW_022994966.1 1 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2419:2564:3490_1:N:0:CGCTGTCT+GGTGAGTA NW_022994964.1 245873 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2422:20021:21512_1:N:0:CGCTGTCT+GGTGAGTA NW_022994893.1 1 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2423:32416:14231_1:N:0:CGCTGTCT+GGTGAGTA NW_022994958.1 2 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2460:9995:32236_1:N:0:CGCTGTCT+GGTGAGTA NW_022994817.1 2148 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:2202:13291_1:N:0:CGCTGTCT+GGTGAGTA NW_022994989.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2464:29414:22028_1:N:0:CGCTGTCT+GGTGAGTA NW_022994881.1 520546 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2477:2284:31187_1:N:0:CGCTGTCT+GGTGAGTA NW_022994981.1 62816 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2478:2808:36041_1:N:0:CGCTGTCT+GGTGAGTA NW_022994810.1 3 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2513:23628:36933_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2513:23637:36949_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18130 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2529:2790:13589_1:N:0:CGCTGTCT+GGTGAGTA NW_022994952.1 218897 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2536:6397:31579_1:N:0:CGCTGTAT+GGTGAGTA NW_022994970.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2539:26639:5134_1:N:0:CGCTGTCT+GGTGAGTA NW_022994939.1 324545 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2543:7889:10739_1:N:0:CGCTGTCT+GGTGAGTA NW_022994927.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2546:26512:16063_1:N:0:CGCTGTCT+GGTGAGTA NW_022994904.1 192198 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2551:25283:16438_1:N:0:CGCTGTCT+GGTGAGTA NW_022994956.1 1 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2561:26413:21903_1:N:0:CGCTGTCT+GGTGAGTA NW_022994922.1 83078 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2609:6786:15812_1:N:0:CGCTGTCT+GGTGAGTA NW_022994971.1 30273 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2614:14615:21418_1:N:0:CGCTGTCT+GGTGAGTA NW_022994946.1 333539 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2627:14100:19930_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 18122 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2634:5638:28479_1:N:0:CGCTGTCT+GGTGAGTA NW_022994993.1 225122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2640:14977:14685_1:N:0:CGCTGTCT+GGTGAGTA NW_022994881.1 520519 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2653:8929:29857_1:N:0:CGCTGTCT+GGTGAGTA NW_022994927.1 1 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2659:1307:28338_1:N:0:CGCTGTCT+GGTGAGTA NW_022994978.1 113583 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2672:4164:16595_1:N:0:CGCTGTCT+GGTGAGTA NC_001276.1 2 74728031 reads; of these: 74728031 (100.00%) were paired; of these: 54821682 (73.36%) aligned concordantly 0 times 9022973 (12.07%) aligned concordantly exactly 1 time 10883376 (14.56%) aligned concordantly >1 times 26.64% overall alignment rate 74728031 reads; of these: 74728031 (100.00%) were paired; of these: 54695188 (73.19%) aligned concordantly 0 times 9096575 (12.17%) aligned concordantly exactly 1 time 10936268 (14.63%) aligned concordantly >1 times 26.81% overall alignment rate 74728031 reads; of these: 74728031 (100.00%) were paired; of these: 54811627 (73.35%) aligned concordantly 0 times 9031518 (12.09%) aligned concordantly exactly 1 time 10884886 (14.57%) aligned concordantly >1 times 26.65% overall alignment rate 74728031 reads; of these: 74728031 (100.00%) were paired; of these: 54680569 (73.17%) aligned concordantly 0 times 9103655 (12.18%) aligned concordantly exactly 1 time 10943807 (14.64%) aligned concordantly >1 times 26.83% overall alignment rate Processed 74728031 sequences in total Successfully deleted the temporary files zr3534_4_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_4_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_4_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_4_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 74728031 Number of paired-end alignments with a unique best hit: 45908181 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 16768986 Sequence pairs did not map uniquely: 12050864 Sequence pairs which were discarded because genomic sequence could not be extracted: 102 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11420758 ((converted) top strand) GA/CT/CT: 11501621 (complementary to (converted) top strand) GA/CT/GA: 11533549 (complementary to (converted) bottom strand) CT/GA/GA: 11452151 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1599391484 Total methylated C's in CpG context: 23340714 Total methylated C's in CHG context: 1384115 Total methylated C's in CHH context: 5878620 Total methylated C's in Unknown context: 57442 Total unmethylated C's in CpG context: 184831527 Total unmethylated C's in CHG context: 278458490 Total unmethylated C's in CHH context: 1105498018 Total unmethylated C's in Unknown context: 3919106 C methylated in CpG context: 11.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 16h 21m 13s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_5_R1.fastp-trim.20201202.fq.gz to zr3534_5_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R1.fastp-trim.20201202.fq.gz to zr3534_5_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R1.fastp-trim.20201202.fq.gz (84046138 sequences in total) Writing a C -> T converted version of the input file zr3534_5_R2.fastp-trim.20201202.fq.gz to zr3534_5_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R2.fastp-trim.20201202.fq.gz to zr3534_5_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R2.fastp-trim.20201202.fq.gz (84046138 sequences in total) Input files are zr3534_5_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_5_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_5_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAATTTAATGAAAAATTATTTATATTATAATATATATATATATATTTATATTTTATATAATATTTAAATAATTAATTTTATTATAATTTAATATATTAAAATATATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTATATTAAAAAAATATAATATTTTTATAAAAAATTTATATATATTAAATAATATTAAAAAATATATTTTAATATATTAAATTATAATAAAATTAATTATTTAAATATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_5_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAACTCAATAAAAAATCACTTATATCACAATATATATATATATATTCACACTTTATACAATACTTAAATAACTAACCCTACTATAATTTAACATATTAAAATACACTTTCCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTGTATTAAAAAAGTATGGTATTTTTATAAGGAATTTGTGTATGTTAAATAATGTTGGAAAGTGTATTTTAATATGTTAAATTATAGTAGGGTTAGTTATTTAAGTATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_5_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAACTCAATAAAAAATCACTTATATCACAATATATATATATATATTCACACTTTATACAATACTTAAATAACTAACCCTACTATAATTTAACATATTAAAATACACTTTCCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTGTATTAAAAAAGTATGGTATTTTTATAAGGAATTTGTGTATGTTAAATAATGTTGGAAAGTGTATTTTAATATGTTAAATTATAGTAGGGTTAGTTATTTAAGTATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_5_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAATTTAATGAAAAATTATTTATATTATAATATATATATATATATTTATATTTTATATAATATTTAAATAATTAATTTTATTATAATTTAATATATTAAAATATATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTATATTAAAAAAATATAATATTTTTATAAAAAATTTATATATATTAAATAATATTAAAAAATATATTTTAATATATTAAATTATAATAAAATTAATTATTTAAATATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1120:9950:30279_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18117 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1129:15881:12806_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1130:3106:16297_1:N:0:AATGCGAA+TCCGCCAA NW_022994946.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1139:11189:9189_1:N:0:AATGCGAA+TCCGCCAA NW_022994995.1 62957 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1149:1280:5963_1:N:0:AATGCGAA+TCCGCCAA NW_022994978.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1149:1072:6010_1:N:0:AATGCGAA+TCCGCCAA NW_022994978.1 1 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1168:31512:5306_1:N:0:AATGCGAA+TCCGCCAA NW_022994917.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1171:30337:7216_1:N:0:AATGCGAA+TCCGCCAA NW_022994997.1 297105 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1174:26205:12367_1:N:0:AATGCGAA+TCCGCCAA NW_022994933.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1176:26657:27398_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2142 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1220:23312:6574_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2140 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1240:28818:4523_1:N:0:AATGCGAA+TCCGCCAA NW_022994964.1 245873 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1240:3378:12446_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18149 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1248:17680:27633_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1248:21757:32659_1:N:0:AATGCGAA+TCCGCCAA NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1250:27227:33207_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18126 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1257:1353:31360_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1270:27444:26193_1:N:0:AATGCGAA+TCCGCCAA NW_022994907.1 80347 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1276:6849:36025_1:N:0:AATGCGAA+TCCGCCAA NW_022994935.1 43731 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1301:18918:26459_1:N:0:AATGCGAA+TCCGCCAA NW_022994974.1 36471 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1322:24831:5822_1:N:0:AATGCGAA+TCCGCCAA NW_022994827.1 1 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1331:28438:2644_1:N:0:AATGCGAA+TCCGCCAA NW_022994964.1 245875 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1339:19913:34381_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1347:7337:2206_1:N:0:AATGCGAA+TCCGCCAA NW_022994812.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1354:13322:28635_1:N:0:AATGCGAA+TCCGCCAA NW_022994810.1 2 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1366:29333:17879_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 90118 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:10104:10066_1:N:0:AATGCGAA+TCCGCCAA NW_022994997.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1413:15356:27242_1:N:0:AATGCGAA+TCCGCCAA NW_022994905.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1413:15456:31516_1:N:0:AATGCGAA+TCCGCCAA NW_022994905.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1415:25400:3364_1:N:0:AATGCGAA+TCCGCCAA NW_022994970.1 1 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1440:10212:25441_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18122 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1445:3712:3411_1:N:0:AATGCGAA+TCCGCCAA NW_022994812.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1450:20898:32769_1:N:0:AATGCGAA+TCCGCCAA NW_022994987.1 316347 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1459:22381:22122_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1459:22598:24095_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1461:27145:33786_1:N:0:AATGCGAA+TCCGCCAA NW_022994935.1 43692 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1467:7202:29747_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1473:6668:32518_1:N:0:AATGCGAA+TCCGCCAA NW_022994888.1 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1502:15085:25488_1:N:0:AATGCGAA+TCCGCCAA NW_022994914.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1507:2483:6198_1:N:0:AATGCGAA+TCCGCCAA NW_022994893.1 1 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1526:28022:10347_1:N:0:AATGCGAA+TCCGCCAA NW_022994906.1 24090 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1528:2709:14920_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1539:5873:8876_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 3 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1547:17409:35211_1:N:0:AATGCGAA+TCCGCCAA NW_022994940.1 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1556:18557:12868_1:N:0:AATGCGAA+TCCGCCAA NW_022994971.1 30277 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1563:14199:10081_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1566:1244:2487_1:N:0:AATGCGAA+TCCGCCAA NW_022994827.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1566:21070:12242_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1566:1488:15374_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18140 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1568:26865:19053_1:N:0:AATGCGAA+TCCGCCAA NW_022994910.1 58925 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1568:26178:20275_1:N:0:AATGCGAA+TCCGCCAA NW_022994910.1 58925 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1568:25789:36385_1:N:0:AATGCGAA+TCCGCCAA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1569:24668:35728_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1570:1316:8406_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1574:30201:19727_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1602:13105:30765_1:N:0:AATGCGAA+TCCGCCAA NW_022994839.1 505241 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:31855:25034_1:N:0:AATGCGAA+TCCGCCAA NW_022994946.1 1 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1619:22652:2550_1:N:0:AATGCGAA+TCCGCCAA NW_022994939.1 2 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1641:11559:1188_1:N:0:AATGCGAA+TCCGCCAA NW_022994888.1 2 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1645:3676:21042_1:N:0:AATGCGAA+TCCGCCAA NW_022994792.1 66690 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1648:20103:18646_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18111 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1664:8748:24283_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18130 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2104:30960:12179_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18117 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2114:10719:2644_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2120:9697:1188_1:N:0:AATGCGAA+TCCGCCAA NW_022994940.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2120:3170:6918_1:N:0:AATGCGAA+TCCGCCAA NW_022994958.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2125:8169:32330_1:N:0:AATGCGAA+TCCGCCAA NW_022994926.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2129:15483:21512_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2140:22227:36761_1:N:0:AATGCGAA+TCCGCCAA NW_022994886.1 2 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2144:21215:25394_1:N:0:AATGCGAA+TCCGCCAA NW_022994978.1 1 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:19596:27790_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:20555:28166_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2163:27028:21934_1:N:0:AATGCGAA+TCCGCCAA NW_022994886.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2164:20726:31563_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 1 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2166:2654:2143_1:N:0:AATGCGAA+TCCGCCAA NW_022994805.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2167:20383:6793_1:N:0:AATGCGAA+TCCGCCAA NW_022994964.1 245881 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2174:4191:10003_1:N:0:AATGCGAA+TCCGCCAA NW_022994777.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2174:28583:11318_1:N:0:AATGCGAA+TCCGCCAA NW_022994958.1 172698 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2203:6795:15515_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2209:3577:17550_1:N:0:AATGCGAA+TCCGCCAA NW_022994997.1 297111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2209:4119:20087_1:N:0:AATGCGAA+TCCGCCAA NW_022994997.1 297109 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2212:23737:20118_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2142 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2212:5023:20995_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2218:30065:33552_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63869 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2218:30635:35070_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63869 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2237:19849:3521_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2142 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2255:5864:14779_1:N:0:AATGCGAA+TCCGCCAA NW_022994974.1 3 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2277:28492:3270_1:N:0:AATGCGAA+TCCGCCAA NW_022994997.1 297105 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2305:30572:36933_1:N:0:AATGCGAA+TCCGCCAA NW_022994915.1 2 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2322:25039:18396_1:N:0:AATGCGAA+TCCGCCAA NW_022994827.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2323:16758:32988_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63844 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2324:23384:36385_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18109 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2330:13268:33708_1:N:0:AATGCGAA+TCCGCCAA NW_022994966.1 514634 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2338:5032:7639_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18113 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2340:20066:5963_1:N:0:AATGCGAA+TCCGCCAA NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2343:32832:2018_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18116 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2373:21866:4601_1:N:0:AATGCGAA+TCCGCCAA NW_022994786.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2374:28366:20682_1:N:0:AATGCGAA+TCCGCCAA NW_022994810.1 3 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2403:16920:4648_1:N:0:AATGCGAA+TCCGCCAA NW_022994956.1 433829 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2412:24361:18537_1:N:0:AATGCGAA+TCCGCCAA NW_022994946.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2416:8666:8954_1:N:0:AATGCGAA+TCCGCCAA NW_022994918.1 404634 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2417:17128:24674_1:N:0:AATGCGAA+TCCGCCAA NW_022994937.1 490594 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2426:17589:5619_1:N:0:AATGCGAA+TCCGCCAA NW_022994932.1 123767 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2427:18186:4742_1:N:0:AATGCGAA+TCCGCCAA NW_022994814.1 2 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2438:11460:24439_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18147 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2444:12500:18349_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18126 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2473:3947:17033_1:N:0:AATGCGAA+TCCGCCAA NW_022994888.1 1 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2518:9851:34616_1:N:0:AATGCGAA+TCCGCCAA NW_022994792.1 66675 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2534:9851:19429_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2543:30147:3161_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2543:29134:3411_1:N:0:AATGCGAA+TCCGCCAA NW_022994817.1 2140 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2553:5864:9298_1:N:0:AATGCGAA+TCCGCCAA NW_022994920.1 2 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2576:13232:8970_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63844 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2576:12906:9815_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63844 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2602:30427:15515_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18109 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2602:30517:18114_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18109 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2602:30517:18145_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18109 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2602:13919:23124_1:N:0:AATGCGAA+TCCGCCAA NW_022994839.1 505241 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2604:31584:21183_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63857 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2615:21350:2300_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2615:21269:2221_1:N:0:AATGCGAA+TCCGCCAA NC_001276.1 18110 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2630:6460:26083_1:N:0:AATGCGAA+TCCGCCAA NW_022994854.1 271220 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2630:29857:27931_1:N:0:AATGCGAA+TCCGCCAA NC_047568.1 57541531 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2632:2184:10066_1:N:0:AATGCGAA+TCCGCCAA NW_022994944.1 261212 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2641:8305:8015_1:N:0:AATGCGAA+TCCGCCAA NW_022994893.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2642:25084:15123_1:N:0:AATGCGAA+TCCGCCAA NW_022994898.1 63869 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2646:31367:20525_1:N:0:AATGCGAA+TCCGCCAA NW_022994819.1 1 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2662:7988:9439_1:N:0:AATGCGAA+TCCGCCAA NW_022994902.1 2 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2669:18457:31861_1:N:0:AATGCGAA+TCCGCCAA NW_022994915.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2678:5077:3270_1:N:0:AATGCGAA+TCCGCCAA NW_022994958.1 172697 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2678:3351:8453_1:N:0:AATGCGAA+TCCGCCAA NW_022994881.1 520553 Processed 84000000 sequence pairs so far 84046138 reads; of these: 84046138 (100.00%) were paired; of these: 61523592 (73.20%) aligned concordantly 0 times 10144494 (12.07%) aligned concordantly exactly 1 time 12378052 (14.73%) aligned concordantly >1 times 26.80% overall alignment rate 84046138 reads; of these: 84046138 (100.00%) were paired; of these: 61504626 (73.18%) aligned concordantly 0 times 10157206 (12.09%) aligned concordantly exactly 1 time 12384306 (14.74%) aligned concordantly >1 times 26.82% overall alignment rate 84046138 reads; of these: 84046138 (100.00%) were paired; of these: 61502003 (73.18%) aligned concordantly 0 times 10148597 (12.08%) aligned concordantly exactly 1 time 12395538 (14.75%) aligned concordantly >1 times 26.82% overall alignment rate 84046138 reads; of these: 84046138 (100.00%) were paired; of these: 61535052 (73.22%) aligned concordantly 0 times 10145932 (12.07%) aligned concordantly exactly 1 time 12365154 (14.71%) aligned concordantly >1 times 26.78% overall alignment rate Processed 84046138 sequences in total Successfully deleted the temporary files zr3534_5_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_5_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_5_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_5_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 84046138 Number of paired-end alignments with a unique best hit: 51605460 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 18775249 Sequence pairs did not map uniquely: 13665429 Sequence pairs which were discarded because genomic sequence could not be extracted: 131 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 12883364 ((converted) top strand) GA/CT/CT: 12873781 (complementary to (converted) top strand) GA/CT/GA: 12919828 (complementary to (converted) bottom strand) CT/GA/GA: 12928356 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1797447404 Total methylated C's in CpG context: 26305415 Total methylated C's in CHG context: 1561214 Total methylated C's in CHH context: 6629878 Total methylated C's in Unknown context: 63671 Total unmethylated C's in CpG context: 207531853 Total unmethylated C's in CHG context: 312507188 Total unmethylated C's in CHH context: 1242911856 Total unmethylated C's in Unknown context: 4404409 C methylated in CpG context: 11.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 17h 34m 18s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_6_R1.fastp-trim.20201202.fq.gz to zr3534_6_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R1.fastp-trim.20201202.fq.gz to zr3534_6_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R1.fastp-trim.20201202.fq.gz (75321697 sequences in total) Writing a C -> T converted version of the input file zr3534_6_R2.fastp-trim.20201202.fq.gz to zr3534_6_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R2.fastp-trim.20201202.fq.gz to zr3534_6_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R2.fastp-trim.20201202.fq.gz (75321697 sequences in total) Input files are zr3534_6_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_6_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_6_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 99 NC_047563.1_CT_converted 51781561 0 94M = 51781551 -104 TTTTTTGGATTTTTTATTTGAGGGGTTAGTTTTTTTTTTTTGATTTTAAAGAAAATGTTTTGTAAAAAGAAATTTTTTGTATATTATATGTTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:8T57T11T15 YS:i:-24 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 147 NC_047563.1_CT_converted 51781551 0 94M = 51781561 104 GATTTTAAAGTTTTTTGGATTTTTTATTTGAGGGGTTAGTTTTTTTTTTTTGATTTTAAAGAAAATGTTTTGTAAAAAGAAATTTTTTGTATAT ,F:FF::FF:::::,,F:F:FF:F:F,FFFF:F,F:FFF,FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G10T57T11T5 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_6_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 77 * 0 0 * * 0 0 TTTTTTAAATTTTTTATTTAAAAAATTAATTTTTTTTTTTTAATTTTAAAAAAAATATTTTATAAAAAAAAATTTTTTATATATTATATATTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 141 * 0 0 * * 0 0 ATATATAAAAAATTTTTTTTTATAAAATATTTTTTTTAAAATTAAAAAAAAAAAATTAATTTTTTAAATAAAAAATTTAAAAAATTTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_6_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 77 * 0 0 * * 0 0 TTTTTTAAATTTTTTATTTAAAAAATTAATTTTTTTTTTTTAATTTTAAAAAAAATATTTTATAAAAAAAAATTTTTTATATATTATATATTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 141 * 0 0 * * 0 0 ATATATAAAAAATTTTTTTTTATAAAATATTTTTTTTAAAATTAAAAAAAAAAAATTAATTTTTTAAATAAAAAATTTAAAAAATTTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_6_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 83 NC_047563.1_GA_converted 8169680 0 94M = 8169690 104 AAAACATATAATATACAAAAAATTTCTTTTTACAAAACATTTTCTTTAAAATCAAAAAAAAAAAACTAACCCCTCAAATAAAAAATCCAAAAAA FFFF,FFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:15A11A57A8 YS:i:-24 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 163 NC_047563.1_GA_converted 8169690 0 94M = 8169680 -104 ATATACAAAAAATTTCTTTTTACAAAACATTTTCTTTAAAATCAAAAAAAAAAAACTAACCCCTCAAATAAAAAATCCAAAAAACTTTAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:5A11A57A10C7 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1106:27344:1438_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1108:29677:11522_1:N:0:AATTCTTG+AAGTTGAC NW_022994978.1 113585 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1113:8612:17159_1:N:0:AATTCTTG+AAGTTGAC NW_022994997.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1132:30761:1031_1:N:0:AATTCTTG+NAGTTGAC NC_001276.1 18130 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1145:18267:31313_1:N:0:AATTCTTG+AAGTTGAC NW_022994916.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1161:10556:6496_1:N:0:AATTCTTG+AAGTTGAC NW_022994778.1 761862 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1204:4327:14998_1:N:0:AATTCTTG+AAGTTGAC NW_022994933.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1204:4924:15749_1:N:0:AATTCTTG+AAGTTGAC NW_022994933.1 2 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1227:13331:15092_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18116 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1237:1145:25050_1:N:0:AATTCTTG+AAGTTGAC NW_022994978.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1244:6994:3208_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18130 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1251:4056:15906_1:N:0:AATTCTTG+AAGTTGAC NW_022994970.1 36331 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1260:5864:4820_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1264:26874:24956_1:N:0:AATTCTTG+AAGTTGAC NW_022994970.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1272:21151:20400_1:N:0:AATTCTTG+AAGTTGAC NW_022994888.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1276:17029:33583_1:N:0:AATTCTTG+AAGTTGAC NW_022994902.1 2 Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1321:6017:26631_1:N:0:AATTCTTG+AAGTTGAC NW_022994987.1 316389 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1321:6858:28369_1:N:0:AATTCTTG+AAGTTGAC NW_022994987.1 316389 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1355:6596:33301_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1359:20835:1939_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1364:5376:21449_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18116 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:29613:29481_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520521 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1402:6470:1485_1:N:0:AATTCTTG+AAGTTGAC NW_022994906.1 24095 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1403:6813:1391_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1411:13792:34710_1:N:0:AATTCTTG+AAGTTGAC NW_022994958.1 172707 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1434:28700:20948_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1437:16062:3192_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1439:2754:14465_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18112 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1448:6271:8876_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1461:10420:9173_1:N:0:AATTCTTG+AAGTTGAC NW_022994944.1 261203 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1466:31141:22670_1:N:0:AATTCTTG+AAGTTGAC NW_022994916.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1478:6225:7357_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1502:29351:25770_1:N:0:AATTCTTG+AAGTTGAC NW_022994944.1 261225 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1512:26829:31798_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1522:14317:17425_1:N:0:AATTCTTG+AAGTTGAC NW_022994792.1 66677 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1538:16866:35493_1:N:0:AATTCTTG+AAGTTGAC NW_022994965.1 30581 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1546:23936:28009_1:N:0:AATTCTTG+AAGTTGAC NW_022994934.1 161470 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1573:24722:29684_1:N:0:AATTCTTG+AAGTTGAC NW_022994939.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1603:3667:31266_1:N:0:AATTCTTG+AAGTTGAC NW_022994819.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:28049:33724_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520548 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:25048:36511_1:N:0:AATTCTTG+AAGTTGAC NW_022994958.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1605:2067:36010_1:N:0:AATTCTTG+AAGTTGAC NW_022994816.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1605:2076:36025_1:N:0:AATTCTTG+AAGTTGAC NW_022994816.1 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1609:27615:18004_1:N:0:AATTCTTG+AAGTTGAC NW_022994965.1 30581 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1614:32000:16548_1:N:0:AATTCTTG+AAGTTGAC NW_022994919.1 196128 Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1642:26087:8437_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1653:3486:21057_1:N:0:AATTCTTG+AAGTTGAC NW_022994792.1 66696 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1670:1777:27430_1:N:0:AATTCTTG+AAGTTGAC NW_022994946.1 333530 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1672:11903:16125_1:N:0:AATTCTTG+AAGTTGAC NW_022994911.1 1 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2108:12943:25535_1:N:0:AATTCTTG+AAGTTGAC NW_022994786.1 2 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2125:13810:9157_1:N:0:AATTCTTG+AAGTTGAC NW_022994964.1 1 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2139:30255:20228_1:N:0:AATTCTTG+AAGTTGAC NW_022994946.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2139:30852:20948_1:N:0:AATTCTTG+AAGTTGAC NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2139:10890:25175_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18110 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2154:12771:11303_1:N:0:AATTCTTG+AAGTTGAC NW_022994952.1 218897 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2154:11831:25238_1:N:0:AATTCTTG+AAGTTGAC NW_022994985.1 189994 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2156:10411:28855_1:N:0:AATTCTTG+AAGTTGAC NW_022994946.1 333527 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2167:9082:16250_1:N:0:AATTCTTG+AAGTTGAC NW_022994778.1 761862 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2168:16080:2347_1:N:0:AATTCTTG+AAGTTGAC NW_022994970.1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2241:1524:21793_1:N:0:AATTCTTG+AAGTTGAC NW_022994881.1 520520 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2248:12536:30467_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18110 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2249:11568:30514_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 1 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2264:21215:4038_1:N:0:AATTCTTG+AAGTTGAC NW_022994975.1 1 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2304:28393:36479_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18124 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2305:6180:27226_1:N:0:AATTCTTG+AAGTTGAC NW_022994907.1 80343 Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2334:27570:25160_1:N:0:AATTCTTG+AAGTTGAC NW_022994899.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2339:24795:23547_1:N:0:AATTCTTG+AAGTTGAC NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2344:1533:10285_1:N:0:AATTCTTG+AAGTTGAC NW_022994786.1 1 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2369:1154:26318_1:N:0:AATTCTTG+AAGTTGAC NW_022994786.1 1 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2403:31331:11913_1:N:0:AATTCTTA+AAGTTGGC NC_001276.1 3 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2434:29821:9424_1:N:0:AATTCTTG+AAGTTGAC NW_022994817.1 2147 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2434:31910:16955_1:N:0:AATTCTTG+AAGTTGAC NW_022994817.1 2150 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2434:2908:33332_1:N:0:AATTCTTG+AAGTTGAC NW_022994978.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2436:20338:35744_1:N:0:AATTCTTG+AAGTTGAC NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2443:3043:8077_1:N:0:AATTCTTG+AAGTTGAC NW_022994966.1 1 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2472:4038:17816_1:N:0:AATTCTTG+AAGTTGAC NW_022994832.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2474:9941:18615_1:N:0:AATTCTTG+AAGTTGAC NW_022994886.1 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2511:28971:7670_1:N:0:AATTCTTG+AAGTTGAC NW_022994786.1 1 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2523:26042:20509_1:N:0:AATTCTTG+AAGTTGAC NW_022994946.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2523:14172:30827_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2525:15628:12962_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 2 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2549:28845:10488_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18117 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2618:21685:2347_1:N:0:AATTCTTG+AAGTTGAC NC_001276.1 18116 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2633:28013:24205_1:N:0:AATTCTTG+AAGTTGAC NW_022994904.1 192219 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2653:2618:14606_1:N:0:AATTCTTG+AAGTTGAC NW_022994792.1 66696 Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far 75321697 reads; of these: 75321697 (100.00%) were paired; of these: 55485192 (73.66%) aligned concordantly 0 times 9041212 (12.00%) aligned concordantly exactly 1 time 10795293 (14.33%) aligned concordantly >1 times 26.34% overall alignment rate 75321697 reads; of these: 75321697 (100.00%) were paired; of these: 55546971 (73.75%) aligned concordantly 0 times 9000097 (11.95%) aligned concordantly exactly 1 time 10774629 (14.30%) aligned concordantly >1 times 26.25% overall alignment rate 75321697 reads; of these: 75321697 (100.00%) were paired; of these: 55520084 (73.71%) aligned concordantly 0 times 9021922 (11.98%) aligned concordantly exactly 1 time 10779691 (14.31%) aligned concordantly >1 times 26.29% overall alignment rate 75321697 reads; of these: 75321697 (100.00%) were paired; of these: 55507187 (73.69%) aligned concordantly 0 times 9027638 (11.99%) aligned concordantly exactly 1 time 10786872 (14.32%) aligned concordantly >1 times 26.31% overall alignment rate Processed 75321697 sequences in total Successfully deleted the temporary files zr3534_6_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_6_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_6_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_6_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 75321697 Number of paired-end alignments with a unique best hit: 45769591 Mapping efficiency: 60.8% Sequence pairs with no alignments under any condition: 17726228 Sequence pairs did not map uniquely: 11825878 Sequence pairs which were discarded because genomic sequence could not be extracted: 85 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11411558 ((converted) top strand) GA/CT/CT: 11429132 (complementary to (converted) top strand) GA/CT/GA: 11471646 (complementary to (converted) bottom strand) CT/GA/GA: 11457170 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1601850100 Total methylated C's in CpG context: 21471982 Total methylated C's in CHG context: 1356883 Total methylated C's in CHH context: 5810020 Total methylated C's in Unknown context: 54542 Total unmethylated C's in CpG context: 186450650 Total unmethylated C's in CHG context: 277897763 Total unmethylated C's in CHH context: 1108862802 Total unmethylated C's in Unknown context: 3983886 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 15h 55m 50s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_7_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_7_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_7_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_7_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_7_R1.fastp-trim.20201202.fq.gz to zr3534_7_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R1.fastp-trim.20201202.fq.gz to zr3534_7_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R1.fastp-trim.20201202.fq.gz (66080050 sequences in total) Writing a C -> T converted version of the input file zr3534_7_R2.fastp-trim.20201202.fq.gz to zr3534_7_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R2.fastp-trim.20201202.fq.gz to zr3534_7_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R2.fastp-trim.20201202.fq.gz (66080050 sequences in total) Input files are zr3534_7_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_7_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_7_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTTAATTAAAATAATTTTTTTTAAAATTATATATTATTTTATTTAATTTATTAATAAATAATATTATTTTTTAAAAAAAAAAATTTTTTTTAAAATTATATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATATAATTTTAAAAAAAATTTTTTTTTTTAAAAAATTATATTATTTATTAATAAATTAAATAAAATAATATTTAATTTTAAAAAAAATTATTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_7_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTCAATTAAAACAATTTTTCCTAAAATTACATATTATCTCATTTAATCCATCAATAAATAATATCATTTTTCAAAAAAAAAAATTTTTCCCAAAATCACATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATGTGATTTTGGGAAAAATTTTTTTTTTTGAAAAATTATATTATTTATTGATGGATTAAATGAGATAATATTTAATTTTAGGAAAAATTGTTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_7_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTCAATTAAAACAATTTTTCCTAAAATTACATATTATCTCATTTAATCCATCAATAAATAATATCATTTTTCAAAAAAAAAAATTTTTCCCAAAATCACATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATGTGATTTTGGGAAAAATTTTTTTTTTTGAAAAATTATATTATTTATTGATGGATTAAATGAGATAATATTTAATTTTAGGAAAAATTGTTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_7_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTTAATTAAAATAATTTTTTTTAAAATTATATATTATTTTATTTAATTTATTAATAAATAATATTATTTTTTAAAAAAAAAAATTTTTTTTAAAATTATATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATATAATTTTAAAAAAAATTTTTTTTTTTAAAAAATTATATTATTTATTAATAAATTAAATAAAATAATATTTAATTTTAAAAAAAATTATTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_7_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_7_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1108:14760:22827_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1110:2067:35634_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1112:17390:29888_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18130 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1138:18882:29747_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18126 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1154:9127:28792_1:N:0:TTCCTACA+AGAATTCG NW_022994962.1 3 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1162:28293:17174_1:N:0:TTCCTACA+AGAATTCG NW_022994828.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1162:28330:17174_1:N:0:TTCCTACA+AGAATTCG NW_022994828.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1172:13078:6324_1:N:0:TTCCTACA+AGAATTCG NW_022994907.1 80342 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1220:13856:9612_1:N:0:TTCCTACA+AGAATTCG NW_022994810.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1220:13232:12101_1:N:0:TTCCTACA+AGAATTCG NW_022994810.1 3 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1237:11369:16642_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 1 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1249:22110:9846_1:N:0:TTCCTACA+AGAATTCG NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1249:2709:35806_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18111 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1273:30915:9189_1:N:0:TTCCTACA+AGAATTCG NW_022994810.1 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1277:18774:29434_1:N:0:TTCCTACA+AGAATTCG NW_022994829.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1308:12816:25880_1:N:0:TTCCTACA+AGAATTCG NW_022994978.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1324:4291:19038_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1325:4562:16595_1:N:0:TTCCTACA+AGAATTCG NW_022994940.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1325:2085:17628_1:N:0:TTCCTACA+AGAATTCG NW_022994940.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1328:32768:19319_1:N:0:TTCCTACA+AGAATTCG NW_022994907.1 80342 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1329:25120:17942_1:N:0:TTCCTACA+AGAATTCG NW_022994952.1 218892 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1348:29143:34084_1:N:0:TTCCTACA+AGAATTCG NW_022994978.1 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1373:4200:12242_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1374:2311:9659_1:N:0:TTCCTACA+AGAATTCG NW_022994932.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:26096:2848_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1404:8241:7905_1:N:0:TTCCTACA+AGAATTCG NW_022994908.1 34608 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1407:15302:9392_1:N:0:TTCCTACA+AGAATTCG NW_022994997.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1411:12608:16908_1:N:0:TTCCTACA+AGAATTCG NW_022994937.1 490594 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1429:14136:23970_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1429:14127:24017_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1451:1922:26177_1:N:0:TTCCTACA+AGAATTAG NW_022994906.1 24088 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1451:7871:26991_1:N:0:TTCCTACA+AGAATTCG NW_022994905.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1452:24722:11898_1:N:0:TTCCTACA+AAAATTCG NW_022994911.1 1 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1462:25581:22968_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 2 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1501:32524:19335_1:N:0:TTCCTACA+AGAATTCG NW_022994907.1 80342 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1501:30499:24251_1:N:0:TTCCTACA+AGAATTCG NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1511:25961:34710_1:N:0:TTCCTACA+AGAATTCG NW_022994792.1 66677 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1514:11695:20744_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1523:27453:31156_1:N:0:TTCCTACA+AGAATTCG NW_022994950.1 2 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1533:28067:26365_1:N:0:TTCCTACA+AGAATTCG NW_022994971.1 2 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1555:28501:29747_1:N:0:TTCCTACA+AGAATTCG NW_022994997.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1567:24614:29027_1:N:0:TTCCTACA+AGAATTCG NW_022994916.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:13810:25942_1:N:0:TTCCTACA+AGAATTCG NW_022994909.1 1 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1623:28004:9471_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1630:25491:1141_1:N:0:TTCCTACA+AGAATTCG NW_022994786.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1633:26051:22968_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1642:16206:20322_1:N:0:TTCCTACA+AGAATTCG NW_022994968.1 91884 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1645:10963:23672_1:N:0:TTCCTACA+AGAATTCG NW_022994920.1 2 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1650:5421:12947_1:N:0:TTCCTACA+AGAATTCG NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1650:13892:14528_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1657:24912:25003_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1661:26982:34820_1:N:0:TTCCTACA+AGAATTCG NW_022994970.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1666:31819:4867_1:N:0:TTCCTACA+AGAATTCG NW_022994992.1 107434 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1670:14669:25207_1:N:0:TTCCTACA+AGAATTCG NW_022994908.1 1 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2102:5412:20040_1:N:0:TTCCTACA+AGAATTCG NW_022994871.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2102:9697:31344_1:N:0:TTCCTACA+AGAATTCG NW_022994871.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2108:15139:21480_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2108:16938:22717_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18110 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2124:2492:22060_1:N:0:TTCCTACA+AGAATTCG NW_022994972.1 189639 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2124:1054:22420_1:N:0:TTCCTACA+AGAATTCG NW_022994972.1 189639 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2135:23755:30201_1:N:0:TTCCTACA+AGAATTCG NW_022994817.1 2142 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2135:23140:30514_1:N:0:TTCCTACA+AGAATTCG NW_022994817.1 2142 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2139:6759:22654_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2146:18593:36730_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18142 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2159:22959:8500_1:N:0:TTCCTACA+AGAATTCG NW_022994786.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:15383:14732_1:N:0:TTCCTACA+AGAATTCG NW_022994924.1 127743 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:15383:15201_1:N:0:TTCCTACA+AGAATTCG NW_022994924.1 127743 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2172:11794:18756_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2172:27968:18834_1:N:0:TTCCTACA+AGAATTCG NW_022994939.1 324551 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2174:12924:12571_1:N:0:TTCCTACA+AGAATTCG NW_022994972.1 189639 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2176:25111:3521_1:N:0:TTCCTACA+AGAATTCG NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2176:14036:31594_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18122 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2211:11116:12665_1:N:0:TTCCTACA+AGAATTCG NW_022994793.1 65970 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2211:9390:12743_1:N:0:TTCCTACA+AGAATTCG NW_022994793.1 65970 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2223:21992:32503_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2228:28818:5055_1:N:0:TTCCTACA+AGAATTCG NW_022994974.1 1 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2249:18557:6136_1:N:0:TTCCTACA+AGAATTCG NW_022994911.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2267:12527:4085_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18147 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2267:11207:4648_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18147 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2267:10954:6652_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18147 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2277:19397:15828_1:N:0:TTCCTACA+AGAATTCG NW_022994829.1 3 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2343:25672:4586_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2346:11153:34303_1:N:0:TTCCTACA+AGAATTCG NW_022994911.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2354:11125:5228_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18111 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2355:11514:14418_1:N:0:TTCCTACA+AGAATTCG NW_022994920.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2360:20175:33959_1:N:0:TTCCTACA+AGAATTCG NW_022994909.1 80229 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2363:19994:15828_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 3 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2370:6677:14465_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2372:27968:24596_1:N:0:TTCCTACA+AGAATTTG NC_001276.1 18117 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2419:9932:11490_1:N:0:TTCCTACA+AGAATTCG NW_022994906.1 24090 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2422:28673:31046_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2424:20021:24643_1:N:0:TTCCTACA+AGAATTCG NW_022994871.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2426:3423:21042_1:N:0:TTCCTACA+AGAATTCG NW_022994792.1 66677 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2429:13675:18599_1:N:0:TTCCTACA+AGAATTCG NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2432:15754:17722_1:N:0:TTCCTACA+AGAATTCG NW_022994911.1 90120 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2436:25880:34695_1:N:0:TTCCTACA+AGAATTCG NW_022994940.1 2 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2532:6650:23813_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18126 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2556:11749:1830_1:N:0:TTCCTACA+AGAAATCG NW_022994917.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2557:24957:26240_1:N:0:TTCCTACA+AGAATTCG NW_022994908.1 34606 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2572:32009:32910_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 18122 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2608:15248:36855_1:N:0:TTCCTACA+AGAATTCG NW_022994981.1 62822 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2609:16812:14168_1:N:0:TTCCTACA+AGAATTCG NW_022994981.1 62822 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2611:30327:1125_1:N:0:TTCCTACA+AGAATTCG NW_022994778.1 761877 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2629:24822:28322_1:N:0:TTCCTACA+AGAATTCG NW_022994786.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2632:17725:4257_1:N:0:TTCCTACA+AGAATTCG NW_022994929.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2632:17653:4288_1:N:0:TTCCTACA+AGAATTCG NW_022994929.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2632:18747:4429_1:N:0:TTCCTACA+AGAATTCG NW_022994929.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2632:25816:9627_1:N:0:TTCCTACA+AGAATTCG NW_022994929.1 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2636:30526:14090_1:N:0:TTCCTACA+AGAATTCG NW_022994964.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2641:14371:23594_1:N:0:TTCCTACA+AGAATTCG NC_001276.1 2 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far 66080050 reads; of these: 66080050 (100.00%) were paired; of these: 48596128 (73.54%) aligned concordantly 0 times 7937006 (12.01%) aligned concordantly exactly 1 time 9546916 (14.45%) aligned concordantly >1 times 26.46% overall alignment rate 66080050 reads; of these: 66080050 (100.00%) were paired; of these: 48596453 (73.54%) aligned concordantly 0 times 7944204 (12.02%) aligned concordantly exactly 1 time 9539393 (14.44%) aligned concordantly >1 times 26.46% overall alignment rate 66080050 reads; of these: 66080050 (100.00%) were paired; of these: 48607339 (73.56%) aligned concordantly 0 times 7933026 (12.01%) aligned concordantly exactly 1 time 9539685 (14.44%) aligned concordantly >1 times 26.44% overall alignment rate 66080050 reads; of these: 66080050 (100.00%) were paired; of these: 48601138 (73.55%) aligned concordantly 0 times 7948193 (12.03%) aligned concordantly exactly 1 time 9530719 (14.42%) aligned concordantly >1 times 26.45% overall alignment rate Processed 66080050 sequences in total Successfully deleted the temporary files zr3534_7_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_7_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_7_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_7_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 66080050 Number of paired-end alignments with a unique best hit: 40370046 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 15234187 Sequence pairs did not map uniquely: 10475817 Sequence pairs which were discarded because genomic sequence could not be extracted: 110 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 10080295 ((converted) top strand) GA/CT/CT: 10080848 (complementary to (converted) top strand) GA/CT/GA: 10101750 (complementary to (converted) bottom strand) CT/GA/GA: 10107043 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1403343205 Total methylated C's in CpG context: 18233544 Total methylated C's in CHG context: 1194392 Total methylated C's in CHH context: 5127016 Total methylated C's in Unknown context: 46389 Total unmethylated C's in CpG context: 161678658 Total unmethylated C's in CHG context: 242953310 Total unmethylated C's in CHH context: 974156285 Total unmethylated C's in Unknown context: 3481561 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 13h 43m 49s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_8_R1.fastp-trim.20201202.fq.gz to zr3534_8_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R1.fastp-trim.20201202.fq.gz to zr3534_8_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R1.fastp-trim.20201202.fq.gz (90605411 sequences in total) Writing a C -> T converted version of the input file zr3534_8_R2.fastp-trim.20201202.fq.gz to zr3534_8_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R2.fastp-trim.20201202.fq.gz to zr3534_8_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R2.fastp-trim.20201202.fq.gz (90605411 sequences in total) Input files are zr3534_8_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_8_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_8_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTTTAATAAAATATATTTAATAATTTAAAATTTTTTATATTAAATTTTTATTATTATTATTTAAATTTATATAATAATTAAATTAAAATTTGATAATTAATAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTAAAATAATATTAAATTAATATATAAATTTTTATAAATTAATAATTTTATTATTATATAAAATTATATTAAATATTAATATTATTTTTATAATAATTAATTTTTTTTAA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_8_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 99 NC_047562.1_GA_converted 50728612 42 114M = 50728738 241 TAATTTTTTTCCAATAAAACATATCTAATAACTTAAAATCTTCTATATCAAATTTCCACCACTATTACTTAAACCTACATAACAATTAAATCAAAATTCAATAATCAACAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:59T17T36 YS:i:-6 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 147 NC_047562.1_GA_converted 50728738 42 115M = 50728612 -241 CTAAAAAAAATCAATTACTACAAAAATAATACCAATATCTAACATAATTCCATATAACAATAAAATTATCAATTTACAAAAACCTACATATCAACCTAACATTACCTCAATAAAA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:17A97 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_8_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTCCAATAAAACATATCTAATAACTTAAAATCTTCTATATCAAATTTCCACCACTATTACTTAAACCTACATAACAATTAAATCAAAATTCAATAATCAACAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTGAGGTAATGTTAGGTTGATATGTAGGTTTTTGTAAATTGATAATTTTATTGTTATATGGAATTATGTTAGATATTGGTATTATTTTTGTAGTAATTGATTTTTTTTAG FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_8_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTTTAATAAAATATATTTAATAATTTAAAATTTTTTATATTAAATTTTTATTATTATTATTTAAATTTATATAATAATTAAATTAAAATTTGATAATTAATAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTAAAATAATATTAAATTAATATATAAATTTTTATAAATTAATAATTTTATTATTATATAAAATTATATTAAATATTAATATTATTTTTATAATAATTAATTTTTTTTAA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1111:15212:8578_1:N:0:ATCCAGGT+GCTGACGT NW_022994925.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1119:2871:30452_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1120:17255:23985_1:N:0:ATCCAGGT+GCTGACGT NW_022994945.1 625619 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1129:27055:32534_1:N:0:ATCCAGGT+GCTGACGT NW_022994997.1 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1131:5990:30655_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1148:26802:5478_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1161:31548:15013_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1169:12789:29716_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520568 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1169:12744:32268_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520568 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1205:20862:3302_1:N:0:ATCCAGGT+GCTGACGT NW_022994996.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1205:8151:25755_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1208:31521:11146_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520522 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1219:32515:5384_1:N:0:ATCCAGGT+GCTGACGT NW_022994893.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1222:14760:14716_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1232:27317:22247_1:N:0:ATCCAGGT+GCTGACGT NW_022994970.1 1 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1265:30463:6277_1:N:0:ATCCAGGT+GCTGACGT NW_022994994.1 1 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1276:1796:22639_1:N:0:ATCCAGGT+GCTGACGT NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1307:2899:9486_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1308:21775:16344_1:N:0:ATCCAGGT+GCTGACGT NW_022994974.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1311:22083:8202_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18129 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1311:23502:12383_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18129 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1313:16324:32393_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18108 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1317:29387:8609_1:N:0:ATCCAGGT+GCTGACGT NW_022994997.1 2 Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1331:23656:16407_1:N:0:ATCCAGGT+GCTGACGT NW_022994950.1 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1356:13693:2597_1:N:0:ATCCAGGT+GCTGACGT NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1357:14335:10723_1:N:0:ATCCAGGT+GCTGACGT NW_022994884.1 165228 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1401:9670:18959_1:N:0:ATCCAGGT+GCTGACGT NW_022994958.1 1 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1402:15745:9032_1:N:0:ATCCAGGT+GCTGACGT NW_022994777.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1402:17906:10614_1:N:0:ATCCAGGT+GCTGACGT NW_022994777.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1406:4481:2080_1:N:0:ATCCAGGT+GCTGACGT NW_022994925.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1406:16975:30013_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1406:15953:35540_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1408:4725:24173_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1412:5593:9455_1:N:0:ATCCAGGT+ACTGACGT NW_022994817.1 2152 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1421:19443:29089_1:N:0:ATCCAGGT+GCTGACGT NW_022994958.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1422:22978:21245_1:N:0:ATCCAGGT+GCTGACGT NW_022994911.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1434:26612:26130_1:N:0:ATCCAGGT+GCTGACGT NW_022994939.1 324545 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1447:22146:10316_1:N:0:ATCCAGGT+GCTGACGT NW_022994919.1 196113 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1447:12011:19758_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18117 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1455:22173:2597_1:N:0:ATCCAGGT+GCTGACGT NW_022994966.1 514634 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1510:27642:12226_1:N:0:ATCCAGGT+GCTGACGT NW_022994915.1 2 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1519:22399:19961_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245875 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1528:27082:8155_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1539:26449:1924_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245875 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1539:25690:2143_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245875 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1541:15727:11788_1:N:0:ATCCAGGT+GCTGACGT NW_022994927.1 1 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1560:14787:12540_1:N:0:ATCCAGGT+GCTGACGT NW_022994927.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1562:13919:3677_1:N:0:ATCCAGGT+GCTGACGT NW_022994884.1 165262 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1575:17752:6840_1:N:0:ATCCAGGT+GCTGACGT NW_022994918.1 404635 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1611:11912:29042_1:N:0:ATCCAGGT+GCTGACGT NW_022994903.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1612:7817:23735_1:N:0:ATCCAGGT+GCTGACGT NW_022994997.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1613:29215:5337_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520547 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1617:8386:30765_1:N:0:ATCCAGGT+GCTGACAT NW_022994792.1 66677 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1632:16107:1830_1:N:0:ATCCAGGT+GCTGACGT NW_022994840.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1634:30219:12837_1:N:0:ATCCAGGT+GCTGACGT NW_022994950.1 1 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1647:3938:9815_1:N:0:ATCCAGGT+GGTGACGT NW_022994911.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1655:17381:17065_1:N:0:ATCCAGGT+GCTGACGT NW_022994966.1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2126:30743:27336_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2129:28140:35978_1:N:0:ATCCAGGT+GCTGACGT NW_022994997.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2136:6424:15624_1:N:0:ATCCAGGT+GCTGACGT NW_022994790.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2142:12617:14669_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2148:22209:17566_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2163:15537:25426_1:N:0:ATCCAGGT+GCTGACGT NW_022994911.1 1 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2170:26883:18145_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2173:31241:3364_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 2 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2208:8594:17942_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520520 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2209:28592:33567_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2209:28583:33990_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2209:27896:34585_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2215:17861:10441_1:N:0:ATCCAGGT+GCTGACGT NW_022994893.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2215:17047:14794_1:N:0:ATCCAGGT+GCTGACGT NW_022994893.1 1 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2231:6063:10363_1:N:0:ATCCAGGT+GCTGACGT NW_022994778.1 761934 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2236:28619:20024_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2236:28339:20854_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2236:27706:22827_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2236:27977:22827_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2249:30653:16282_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2252:17779:7044_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2255:5303:35509_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18111 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2265:19280:1219_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2274:25997:11193_1:N:0:ATCCAGGT+GCTGACGT NW_022994939.1 324548 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2277:11496:4210_1:N:0:ATCCAGGT+GCTGACGT NW_022994837.1 686288 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2307:1588:19899_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2309:25961:4523_1:N:0:ATCCAGGT+GCTGACGT NW_022994939.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2310:14073:1188_1:N:0:ATCCAGGT+GCTGACGT NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2310:14362:3599_1:N:0:ATCCAGGT+GCTGACGT NW_022994958.1 1 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2315:8332:9126_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 333527 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2315:8929:10034_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 333527 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2317:26684:24126_1:N:0:ATCCAGGT+GCTGACGT NW_022994997.1 2 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2336:16288:6402_1:N:0:ATCCAGGT+GCTGACGT NW_022994864.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2337:21459:21966_1:N:0:ATCCAGGT+GCTGACGT NW_022994923.1 61826 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2341:24605:8218_1:N:0:ATCCAGGT+GCTGACGT NW_022994961.1 1 Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2344:27561:29340_1:N:0:ATCCAGGT+GCTGACGT NW_022994957.1 201032 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2346:5502:15154_1:N:0:ATCCAGGT+GCTGACGT NW_022994960.1 1 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2364:10854:22639_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 2 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2375:7057:16344_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 1 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2402:15772:1532_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2403:27769:31579_1:N:0:ATCCAGGT+GCTGACGT NW_022994913.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2405:15103:29622_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2407:8992:11929_1:N:0:ATCCAGGT+GCTGACGT NW_022994802.1 3 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2410:19361:26819_1:N:0:ATCCAGGT+GCTGACGT NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2412:17363:5760_1:N:0:ATCCAGGT+GCTGACGT NW_022994810.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2412:16360:5995_1:N:0:ATCCAGGT+GCTGACGT NW_022994810.1 1 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2424:19208:26897_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18149 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2429:12418:32737_1:N:0:ATCCAGGT+GCTGACGT NW_022994957.1 201108 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:24822:13542_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18114 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2461:23710:18161_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18114 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2463:4209:26412_1:N:0:ATCCAGGT+GCTGACGT NW_022994810.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2467:29550:31250_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2471:10755:11287_1:N:0:ATCCAGGT+GCTGACGT NW_022994911.1 2 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2478:20193:19836_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18116 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2478:25427:28714_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520548 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:29966:2942_1:N:0:ATCCGGGT+GCTGACGT NW_022994810.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:7401:20979_1:N:0:ATCCAGGT+GCTGACGT NW_022994817.1 2140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2502:15185:30264_1:N:0:ATCCAGGT+GCTGACGT NW_022994817.1 2140 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2505:27037:16971_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245874 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2505:27398:20165_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245873 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2521:23863:1110_1:N:0:ATCCAGGT+GCTGACGT NW_022994966.1 514632 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2528:15745:11099_1:N:0:ATCCAGGT+GCTGACGT NW_022994819.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2528:13367:15875_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18140 Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2564:28456:31485_1:N:0:ATCCAGGT+GCTGACGT NW_022994920.1 2 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2573:32000:7247_1:N:0:ATCCAGGT+GCTGACGT NW_022994909.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2575:16721:11725_1:N:0:ATCCAGGT+GCTGACGT NW_022994918.1 404635 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2575:23077:33880_1:N:0:ATCCAGGT+GCTGACGT NC_001276.1 18109 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2578:30897:11757_1:N:0:ATCCAGGT+GCTGACGT NW_022994920.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2578:14543:22795_1:N:0:ATCCAGGT+GCTGACGT NW_022994965.1 30578 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2635:6017:23062_1:N:0:ATCCAGGT+GCTGACGT NW_022994945.1 625619 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2640:5629:14591_1:N:0:ATCCAGGT+GCTGACGT NW_022994964.1 245873 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2654:4001:2691_1:N:0:ATCCAGGT+GCTGACGT NW_022994970.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2654:7527:13777_1:N:0:ATCCAGGT+GCTGACGT NW_022994970.1 2 Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2664:14913:12007_1:N:0:ATCCAGGT+GCTGACGT NW_022994951.1 2 Processed 90000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2676:20952:15515_1:N:0:ATCCAGGT+GCTGACGT NW_022994881.1 520547 90605411 reads; of these: 90605411 (100.00%) were paired; of these: 66431763 (73.32%) aligned concordantly 0 times 10843572 (11.97%) aligned concordantly exactly 1 time 13330076 (14.71%) aligned concordantly >1 times 26.68% overall alignment rate 90605411 reads; of these: 90605411 (100.00%) were paired; of these: 66417249 (73.30%) aligned concordantly 0 times 10848724 (11.97%) aligned concordantly exactly 1 time 13339438 (14.72%) aligned concordantly >1 times 26.70% overall alignment rate 90605411 reads; of these: 90605411 (100.00%) were paired; of these: 66104207 (72.96%) aligned concordantly 0 times 11011544 (12.15%) aligned concordantly exactly 1 time 13489660 (14.89%) aligned concordantly >1 times 27.04% overall alignment rate 90605411 reads; of these: 90605411 (100.00%) were paired; of these: 66093240 (72.95%) aligned concordantly 0 times 11007343 (12.15%) aligned concordantly exactly 1 time 13504828 (14.91%) aligned concordantly >1 times 27.05% overall alignment rate Processed 90605411 sequences in total Successfully deleted the temporary files zr3534_8_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_8_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_8_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_8_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 90605411 Number of paired-end alignments with a unique best hit: 55543581 Mapping efficiency: 61.3% Sequence pairs with no alignments under any condition: 20159676 Sequence pairs did not map uniquely: 14902154 Sequence pairs which were discarded because genomic sequence could not be extracted: 132 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 13773128 ((converted) top strand) GA/CT/CT: 13966090 (complementary to (converted) top strand) GA/CT/GA: 13998198 (complementary to (converted) bottom strand) CT/GA/GA: 13806033 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1919611382 Total methylated C's in CpG context: 25390230 Total methylated C's in CHG context: 1605629 Total methylated C's in CHH context: 6877825 Total methylated C's in Unknown context: 64253 Total unmethylated C's in CpG context: 221478350 Total unmethylated C's in CHG context: 332078494 Total unmethylated C's in CHH context: 1332180854 Total unmethylated C's in Unknown context: 4697286 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 18h 48m 29s ==================== Bismark run complete ==================== Use of uninitialized value $path_to_bowtie in concatenation (.) or string at /gscratch/srlab/programs/Bismark-0.21.0/bismark line 6893. Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.1.0]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/030521-ronrosM'): /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/030521-ronrosM Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file zr3534_9_R1.fastp-trim.20201202.fq.gz to zr3534_9_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R1.fastp-trim.20201202.fq.gz to zr3534_9_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R1.fastp-trim.20201202.fq.gz (73776588 sequences in total) Writing a C -> T converted version of the input file zr3534_9_R2.fastp-trim.20201202.fq.gz to zr3534_9_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R2.fastp-trim.20201202.fq.gz to zr3534_9_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R2.fastp-trim.20201202.fq.gz (73776588 sequences in total) Input files are zr3534_9_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_9_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_9_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TGGTATTATTTAAAGTTTTGGGGGTATGTTTGTGGATTGTGGATGTTTTGTTTATTTGTAGGATGTTGTTTTTTGGATGTGTTAGTTTTTTAGTTTTAGTAAAAAAGATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATCTTTTTTACTAAAACTAAAAAACTAACACATCCAAAAAACAACATCCTACAAATAAACAAAACATCCACAATCCACAAACATACCCCCAAAACTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_9_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TAATATTATTTAAAATTTTAAAAATATATTTATAAATTATAAATATTTTATTTATTTATAAAATATTATTTTTTAAATATATTAATTTTTTAATTTCAATAAAAAAAATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATTTTTTTTATTGAAATTAAAAAATTAATATATTTAAAAAATAATATTTTATAAATAAATAAAATATTTATAATTTATAAATATATTTTTAAAATTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_9_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TAATATTATTTAAAATTTTAAAAATATATTTATAAATTATAAATATTTTATTTATTTATAAAATATTATTTTTTAAATATATTAATTTTTTAATTTCAATAAAAAAAATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATTTTTTTTATTGAAATTAAAAAATTAATATATTTAAAAAATAATATTTTATAAATAAATAAAATATTTATAATTTATAAATATATTTTTAAAATTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_9_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TGGTATTATTTAAAGTTTTGGGGGTATGTTTGTGGATTGTGGATGTTTTGTTTATTTGTAGGATGTTGTTTTTTGGATGTGTTAGTTTTTTAGTTTTAGTAAAAAAGATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATCTTTTTTACTAAAACTAAAAAACTAACACATCCAAAAAACAACATCCTACAAATAAACAAAACATCCACAATCCACAAACATACCCCCAAAACTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1101:12671:33426_1:N:0:CTTATTGG+ACTTGTTA NW_022994786.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1104:24569:26099_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1106:4218:7764_1:N:0:CTTATTGG+ACTTGTTA NW_022994952.1 218897 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1107:25654:15201_1:N:0:CTTATTGG+ACTTGTTA NW_022994917.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1107:3414:15358_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1108:17273:28870_1:N:0:CTTATTGG+ACTTGTTA NW_022994911.1 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1145:1072:36104_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1152:16125:3928_1:N:0:CTTATTGG+ACTTGTTA NW_022994881.1 520520 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1152:14552:13072_1:N:0:CTTATTGG+ACTTGTTA NW_022994944.1 261202 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1152:18837:26569_1:N:0:CTTATTGG+ACTTGTTA NW_022994944.1 261202 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1153:9127:19147_1:N:0:CTTATTGG+ACTTGTTA NW_022994950.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1164:19849:17832_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18117 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1165:13512:32221_1:N:0:CTTATTGG+ACTTGTTA NW_022994908.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1175:11433:29215_1:N:0:CTTATTGG+ACTTGTTA NW_022994793.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1176:28293:9565_1:N:0:CTTATTGG+ACTTGTTA NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1176:27868:9580_1:N:0:CTTATTGG+ACTTGTTA NW_022994911.1 1 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1176:23303:31109_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1209:5475:3364_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1209:8594:9925_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1213:16288:1517_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1218:13910:8484_1:N:0:CTTATTGG+ACTTGTTA NW_022994934.1 161487 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1243:19587:36667_1:N:0:CTTATTGG+ACTTGTTA NW_022994933.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1247:7256:30624_1:N:0:CTTATTGG+ACTTGTTA NW_022994931.1 118215 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1267:21531:15702_1:N:0:CTTATTGG+ACTTGTTA NW_022994931.1 118215 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1267:23393:16705_1:N:0:CTTATTGG+ACTTGTTA NW_022994931.1 118215 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1269:18900:30561_1:N:0:CTTATTGG+ACTTGTTA NW_022994911.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1270:22019:2801_1:N:0:CTTATTGG+ACTTGTTA NW_022994898.1 63841 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1270:17842:19805_1:N:0:CTTATTGG+ACTTGTTA NW_022994905.1 1 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1276:21187:13166_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18116 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1312:16586:17347_1:N:0:CTTATTGG+ACTTGTTA NW_022994939.1 324543 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1319:24388:12727_1:N:0:CTTATTGG+ACTTGTTA NW_022994903.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1319:25997:13886_1:N:0:CTTATTGG+ACTTGTTA NW_022994903.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1320:14091:11397_1:N:0:CTTATTGG+ACTTGTTA NW_022994810.1 3 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1326:30933:4147_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18110 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1332:5674:14356_1:N:0:CTTATTGG+ACTTGTTA NW_022994929.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1334:5999:13730_1:N:0:CTTATTGG+ACTTGTTA NW_022994939.1 324548 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1356:18602:9439_1:N:0:CTTATTGG+ACTTGTTA NW_022994790.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1356:22309:13917_1:N:0:CTTATTGG+ACTTGTTA NW_022994936.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1359:18186:2487_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18111 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1360:12698:14873_1:N:0:CTTATTGG+ACTTGTTA NW_022994935.1 43684 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1360:21296:15201_1:N:0:CTTATTGG+ACTTGTTA NW_022994935.1 43684 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1369:24686:15812_1:N:0:CTTATTGG+ACTTGTTA NW_022994987.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1403:30138:35055_1:N:0:CTTATTGG+ACTTGTTA NW_022994958.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1405:14353:30671_1:N:0:CTTATTGG+ACTTGTTA NW_022994910.1 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1422:15546:24752_1:N:0:CTTATTGG+ACTTGTTA NW_022994970.1 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1436:14986:1391_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1436:14724:1846_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1439:24795:14685_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1444:16568:29089_1:N:0:CTTATTGG+ACTTGTTA NW_022994905.1 1 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1452:11261:36025_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1459:29604:3537_1:N:0:CTTATTGG+ACTTGTTA NW_022994881.1 520519 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1469:12762:7310_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 1 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1506:11225:10066_1:N:0:CTTATTGG+ACTTGTTA NW_022994953.1 45795 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1507:9507:7560_1:N:0:CTTATTGG+ACTTGTTA NW_022994819.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1510:7581:32847_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18109 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1525:8115:19742_1:N:0:CTTATTGG+ACTTGTTA NW_022994909.1 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1532:21079:6934_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1544:21504:33223_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1551:10221:21699_1:N:0:CTTATTGG+ACTTGTTA NW_022994933.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1555:30454:7232_1:N:0:CTTATTGG+ACTTGTTA NW_022994898.1 63853 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1556:5602:15233_1:N:0:CTTATTGG+ACTTGTTA NW_022994939.1 2 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1576:20772:17237_1:N:0:CTTATTGG+ACTTGTTA NW_022994777.1 123425 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1603:22580:15608_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18154 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1603:3504:29450_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1604:6858:9862_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1618:30436:17315_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1637:4354:8813_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1657:15519:1939_1:N:0:CTTATTGG+ACTTGTTA NW_022994966.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1658:13937:14951_1:N:0:CTTATTGG+ACTTGTTA NW_022994933.1 2 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1668:19081:4633_1:N:0:CTTATTGG+ACTTGTTA NW_022994980.1 6458 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1675:24731:30326_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18114 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2116:10664:34021_1:N:0:CTTATTGG+ACTTGTTA NW_022994951.1 187647 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2151:26485:2143_1:N:0:CTTATTGG+ACTTGTTA NW_022994864.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2160:19018:34773_1:N:0:CTTATTGG+ACTTGTTA NW_022994869.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2162:4083:36714_1:N:0:CTTATTGG+ACTTGTTA NW_022994898.1 63842 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2163:29695:29528_1:N:0:CTTATTGG+ACTTGTTA NW_022994966.1 1 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2177:23818:8108_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2213:29423:24893_1:N:0:CTTATTGG+ACTTGTTA NW_022994938.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2215:16423:33692_1:N:0:CTTATTGG+ACTTGTTA NW_022994970.1 2 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2224:12735:8766_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18111 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2260:28899:20322_1:N:0:CTTATTGG+ACTTGTTA NW_022994899.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2260:8992:25363_1:N:0:CTTATTGG+ACTTGTTA NW_022994881.1 520519 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2270:17571:10254_1:N:0:CTTATTGG+ACTTGTTA NW_022994905.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2270:3965:13213_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2307:29297:29653_1:N:0:CTTATTGG+ACTTGTTA NW_022994958.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2308:8413:18975_1:N:0:CTTATTGG+ACTTGTTA NW_022994904.1 192190 Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2312:12635:17456_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2312:19425:25300_1:N:0:CTTATTGG+ACTTGTTA NW_022994939.1 324543 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2319:24587:34460_1:N:0:CTTATTGG+ACTTGTTA NW_022994903.1 2 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2326:31702:24612_1:N:0:CTTATTGG+ACTTGTTA NW_022994962.1 3 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2331:23529:9392_1:N:0:CTTATTGG+ACTTGTTA NW_022994985.1 189987 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2331:24876:20588_1:N:0:CTTATTGG+ACTTGTTA NW_022994985.1 189987 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2333:23647:7905_1:N:0:CTTATTGG+ACTTGTTA NW_022994903.1 1 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2353:1199:25332_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18117 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2353:24641:25817_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18126 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2365:16929:12023_1:N:0:CTTATTGG+ACTTGTTA NW_022994980.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2367:1063:36777_1:N:0:CTTATTGG+ACTTGTTA NW_022994910.1 1 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2406:19578:32894_1:N:0:CTTATTGG+ACTTGTTA NW_022994992.1 107475 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2426:26078:4257_1:N:0:CTTATTGG+ACTTGTTA NW_022994927.1 1 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2430:12536:14716_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18109 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2441:13711:1094_1:N:0:CTTATTGG+NCTTGTTA NW_022994965.1 30581 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2444:2130:2738_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2444:15230:25989_1:N:0:CTTATTGG+ACTTGTTA NW_022994905.1 1 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2466:27308:20885_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2466:25256:27320_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2504:27480:2707_1:N:0:CTTATTGG+ACTTGTTA NW_022994946.1 2 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2505:21929:30232_1:N:0:CTTATTGG+ACTTGTTA NW_022994913.1 18496 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2505:19967:31751_1:N:0:CTTATTGG+ACTTGTTA NW_022994913.1 18496 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2528:24822:25379_1:N:0:CTTATTGG+ACTTGTTA NW_022994985.1 189987 Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2534:11641:17143_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2534:10737:18427_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18122 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2542:15275:9408_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 1 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2563:10438:2722_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 2 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2606:22516:25989_1:N:0:CTTATTGG+ACTTGTTA NW_022994881.1 520521 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2613:2790:34882_1:N:0:CTTATTGG+ACTTGTTA NW_022994905.1 1 Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2618:25726:33708_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18130 Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2620:26413:17519_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2641:18539:31093_1:N:0:CTTATTGG+ACTTGTTA NW_022994881.1 520519 Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2657:31602:32424_1:N:0:CTTATTGG+ACTTGTTA NW_022994917.1 1 Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:2672:26440:36605_1:N:0:CTTATTGG+ACTTGTTA NC_001276.1 18140 73776588 reads; of these: 73776588 (100.00%) were paired; of these: 53811950 (72.94%) aligned concordantly 0 times 9003795 (12.20%) aligned concordantly exactly 1 time 10960843 (14.86%) aligned concordantly >1 times 27.06% overall alignment rate 73776588 reads; of these: 73776588 (100.00%) were paired; of these: 53840202 (72.98%) aligned concordantly 0 times 8990264 (12.19%) aligned concordantly exactly 1 time 10946122 (14.84%) aligned concordantly >1 times 27.02% overall alignment rate 73776588 reads; of these: 73776588 (100.00%) were paired; of these: 53876722 (73.03%) aligned concordantly 0 times 8964856 (12.15%) aligned concordantly exactly 1 time 10935010 (14.82%) aligned concordantly >1 times 26.97% overall alignment rate 73776588 reads; of these: 73776588 (100.00%) were paired; of these: 53852704 (72.99%) aligned concordantly 0 times 8975933 (12.17%) aligned concordantly exactly 1 time 10947951 (14.84%) aligned concordantly >1 times 27.01% overall alignment rate Processed 73776588 sequences in total Successfully deleted the temporary files zr3534_9_R1.fastp-trim.20201202.fq.gz_C_to_T.fastq, zr3534_9_R1.fastp-trim.20201202.fq.gz_G_to_A.fastq, zr3534_9_R2.fastp-trim.20201202.fq.gz_C_to_T.fastq and zr3534_9_R2.fastp-trim.20201202.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 73776588 Number of paired-end alignments with a unique best hit: 45591578 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 16002262 Sequence pairs did not map uniquely: 12182748 Sequence pairs which were discarded because genomic sequence could not be extracted: 120 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 11364394 ((converted) top strand) GA/CT/CT: 11385517 (complementary to (converted) top strand) GA/CT/GA: 11430000 (complementary to (converted) bottom strand) CT/GA/GA: 11411547 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1595529090 Total methylated C's in CpG context: 21006842 Total methylated C's in CHG context: 1277934 Total methylated C's in CHH context: 5350483 Total methylated C's in Unknown context: 49317 Total unmethylated C's in CpG context: 188873033 Total unmethylated C's in CHG context: 281019136 Total unmethylated C's in CHH context: 1098001662 Total unmethylated C's in Unknown context: 3841672 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 15h 22m 20s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 48007551 Total number duplicated alignments removed: 8860696 (18.46%) Duplicated alignments were found at: 7366422 different position(s) Total count of deduplicated leftover sequences: 39146855 (81.54% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 47127628 Total number duplicated alignments removed: 8738807 (18.54%) Duplicated alignments were found at: 7320561 different position(s) Total count of deduplicated leftover sequences: 38388821 (81.46% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 46140823 Total number duplicated alignments removed: 8446870 (18.31%) Duplicated alignments were found at: 7047577 different position(s) Total count of deduplicated leftover sequences: 37693953 (81.69% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 47623611 Total number duplicated alignments removed: 8490542 (17.83%) Duplicated alignments were found at: 7141080 different position(s) Total count of deduplicated leftover sequences: 39133069 (82.17% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 45908079 Total number duplicated alignments removed: 8215841 (17.90%) Duplicated alignments were found at: 6925548 different position(s) Total count of deduplicated leftover sequences: 37692238 (82.10% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 51605329 Total number duplicated alignments removed: 9670187 (18.74%) Duplicated alignments were found at: 8064818 different position(s) Total count of deduplicated leftover sequences: 41935142 (81.26% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 45769506 Total number duplicated alignments removed: 8305093 (18.15%) Duplicated alignments were found at: 6947758 different position(s) Total count of deduplicated leftover sequences: 37464413 (81.85% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 40369936 Total number duplicated alignments removed: 6665992 (16.51%) Duplicated alignments were found at: 5688018 different position(s) Total count of deduplicated leftover sequences: 33703944 (83.49% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_7_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_7_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 55543449 Total number duplicated alignments removed: 11447130 (20.61%) Duplicated alignments were found at: 9375294 different position(s) Total count of deduplicated leftover sequences: 44096319 (79.39% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ 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header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam: 45591458 Total number duplicated alignments removed: 7999205 (17.55%) Duplicated alignments were found at: 6741104 different position(s) Total count of deduplicated leftover sequences: 37592253 (82.45% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz" *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Output will be written to the current directory ('/gscratch/scrubbed/sr320/030521-ronrosM') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_10_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_10_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 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34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 38000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 38500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 37500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 37500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 39000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 38000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 38000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 38500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 38500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 39000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 36500000 Processed lines: 39000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Finished processing child process. Exiting.. Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 39146855 lines in total Total number of methylation call strings processed: 78293710 Final Cytosine Methylation Report ================================= Total number of C's analysed: 942295272 Total methylated C's in CpG context: 12005773 Total methylated C's in CHG context: 727974 Total methylated C's in CHH context: 3110667 Total C to T conversions in CpG context: 110469959 Total C to T conversions in CHG context: 163950124 Total C to T conversions in CHH context: 652030775 C methylated in CpG context: 9.8% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 Now reading in Bismark result file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 7500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 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lines: 11000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 11500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 11500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 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lines: 36000000 Finished processing child process. Exiting.. Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Finished processing child process. Exiting.. Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 38000000 Processed lines: 38000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 38388821 lines in total Total number of methylation call strings processed: 76777642 Final Cytosine Methylation Report ================================= Total number of C's analysed: 923441134 Total methylated C's in CpG context: 12160729 Total methylated C's in CHG context: 771829 Total methylated C's in CHH context: 3314006 Total C to T conversions in CpG context: 106774410 Total C to T conversions in CHG context: 159361439 Total C to T conversions in CHH context: 641058721 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 Now reading in Bismark result file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 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Processed lines: 34000000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 36000000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 35500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 36500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 36000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 36500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 36000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 36500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 36500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 35500000 Processed lines: 37000000 Processed lines: 35000000 Processed lines: 37500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 37000000 Processed lines: 35000000 Finished processing child process. Exiting.. Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 37500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 37500000 Processed lines: 36000000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 37693953 lines in total Total number of methylation call strings processed: 75387906 Final Cytosine Methylation Report ================================= Total number of C's analysed: 911253744 Total methylated C's in CpG context: 12014863 Total methylated C's in CHG context: 763389 Total methylated C's in CHH context: 3276821 Total C to T conversions in CpG context: 105812698 Total C to T conversions in CHG context: 157435632 Total C to T conversions in CHH context: 631950341 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_3_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_3_R2.fastp-trim.20201202.fq.gz" Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 36000000 Processed lines: 38000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 38500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 38500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 39000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 39000000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37500000 Processed lines: 36500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 37000000 Processed lines: 38000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 38500000 Processed lines: 37500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 38000000 Processed lines: 38000000 Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 38000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 38500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 38500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 39000000 Finished processing child process. Exiting.. Processed lines: 39000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 39133069 lines in total Total number of methylation call strings processed: 78266138 Final Cytosine Methylation Report ================================= Total number of C's analysed: 966714974 Total methylated C's in CpG context: 14292801 Total methylated C's in CHG context: 833216 Total methylated C's in CHH context: 3552711 Total C to T conversions in CpG context: 109585647 Total C to T conversions in CHG context: 165674993 Total C to T conversions in CHH context: 672775606 C methylated in CpG context: 11.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 Now reading in Bismark result file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_4_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 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lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 33000000 Processed lines: 36000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 36500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 37000000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 37500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 37692238 lines in total Total number of methylation call strings processed: 75384476 Final Cytosine Methylation Report ================================= Total number of C's analysed: 905767036 Total methylated C's in CpG context: 12781614 Total methylated C's in CHG context: 771949 Total methylated C's in CHH context: 3313636 Total C to T conversions in CpG context: 103354653 Total C to T conversions in CHG context: 155896761 Total C to T conversions in CHH context: 629648423 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_5_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 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lines: 38000000 Processed lines: 38500000 Processed lines: 38000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 41000000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 41000000 Processed lines: 40000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 41000000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 38500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 38500000 Processed lines: 38500000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 41500000 Processed lines: 39000000 Processed lines: 40000000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 39500000 Processed lines: 39000000 Processed lines: 41500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 39000000 Processed lines: 39500000 Processed lines: 39000000 Processed lines: 39000000 Processed lines: 40000000 Finished processing child process. Exiting.. Processed lines: 40000000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 40000000 Finished processing child process. Exiting.. Processed lines: 39500000 Processed lines: 40500000 Processed lines: 40000000 Finished processing child process. Exiting.. Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 41000000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 40000000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 40000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Finished processing child process. Exiting.. Processed lines: 40500000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41000000 Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 41500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 41935142 lines in total Total number of methylation call strings processed: 83870284 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1001853984 Total methylated C's in CpG context: 14205083 Total methylated C's in CHG context: 857017 Total methylated C's in CHH context: 3688422 Total C to T conversions in CpG context: 114075011 Total C to T conversions in CHG context: 172180736 Total C to T conversions in CHH context: 696847715 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_6_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_6_R2.fastp-trim.20201202.fq.gz" Now reading in Bismark result file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 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lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 37000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35500000 Finished processing child process. Exiting.. Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 37464413 lines in total Total number of methylation call strings processed: 74928826 Final Cytosine Methylation Report ================================= Total number of C's analysed: 910669092 Total methylated C's in CpG context: 11841329 Total methylated C's in CHG context: 760115 Total methylated C's in CHH context: 3288745 Total C to T conversions in CpG context: 104532651 Total C to T conversions in CHG context: 156229733 Total C to T conversions in CHH context: 634016519 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_7_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_7_R2.fastp-trim.20201202.fq.gz" Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. 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lines: 30500000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30000000 Processed lines: 30500000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30500000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 33500000 Processed lines: 30000000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 31000000 Finished processing child process. Exiting.. Processed lines: 30500000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 30500000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 31000000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 31500000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32000000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32000000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 32500000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 32500000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33000000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Finished processing child process. Exiting.. Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33500000 Processed lines: 33500000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33000000 Processed lines: 33500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 33000000 Processed lines: 33500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 33500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 33500000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Finished processing child process. Exiting.. Processed lines: 33500000 Processed lines: 33500000 Processed lines: 33500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 33500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 33703944 lines in total Total number of methylation call strings processed: 67407888 Final Cytosine Methylation Report ================================= Total number of C's analysed: 815274441 Total methylated C's in CpG context: 10242157 Total methylated C's in CHG context: 682349 Total methylated C's in CHH context: 2962714 Total C to T conversions in CpG context: 93016354 Total C to T conversions in CHG context: 139619354 Total C to T conversions in CHH context: 568751513 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_8_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_8_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1000000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 1500000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2000000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 2500000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3000000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 3500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 4500000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5000000 Processed lines: 5500000 Processed lines: 5500000 Processed lines: 5000000 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Processed lines: 5500000 Processed lines: 5500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 6500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7500000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 Processed lines: 7000000 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Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 8500000 Processed lines: 8000000 Processed lines: 8000000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 8500000 Processed lines: 9500000 Processed lines: 8500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 10000000 Processed lines: 9000000 Processed lines: 9000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 9500000 Processed lines: 9500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 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40000000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 42500000 Processed lines: 40500000 Processed lines: 39500000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 39500000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 43000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 43000000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 43000000 Processed lines: 40500000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 41000000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40000000 Processed lines: 40500000 Processed lines: 43500000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 43500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 43500000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41500000 Processed lines: 40500000 Processed lines: 40500000 Processed lines: 41000000 Processed lines: 40500000 Processed lines: 44000000 Processed lines: 41500000 Processed lines: 41000000 Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 42000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 44000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41500000 Finished processing child process. Exiting.. Processed lines: 41500000 Processed lines: 44000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 42000000 Finished processing child process. Exiting.. Processed lines: 41000000 Processed lines: 41000000 Processed lines: 41500000 Processed lines: 41000000 Processed lines: 42000000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 41500000 Processed lines: 42000000 Processed lines: 41500000 Processed lines: 42500000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 43000000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 43000000 Processed lines: 42000000 Processed lines: 42500000 Processed lines: 42000000 Processed lines: 42000000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 43000000 Processed lines: 43500000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 43500000 Processed lines: 43000000 Processed lines: 43000000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 43500000 Processed lines: 42500000 Processed lines: 43000000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 42500000 Processed lines: 43500000 Processed lines: 43500000 Processed lines: 43000000 Processed lines: 44000000 Processed lines: 43000000 Processed lines: 43000000 Processed lines: 43500000 Processed lines: 43000000 Processed lines: 43000000 Processed lines: 43000000 Finished processing child process. Exiting.. Processed lines: 43000000 Processed lines: 43000000 Processed lines: 43500000 Processed lines: 43000000 Processed lines: 44000000 Processed lines: 43500000 Processed lines: 43500000 Processed lines: 43500000 Finished processing child process. Exiting.. Processed lines: 43000000 Processed lines: 44000000 Processed lines: 43000000 Processed lines: 43500000 Processed lines: 43000000 Processed lines: 43000000 Finished processing child process. Exiting.. Processed lines: 44000000 Processed lines: 43000000 Processed lines: 44000000 Processed lines: 43500000 Finished processing child process. Exiting.. Processed lines: 43500000 Processed lines: 44000000 Processed lines: 43500000 Processed lines: 43500000 Processed lines: 43500000 Finished processing child process. Exiting.. Processed lines: 43500000 Processed lines: 43500000 Processed lines: 43500000 Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 43500000 Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 44000000 Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 43500000 Processed lines: 43500000 Processed lines: 44000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 43500000 Processed lines: 43500000 Processed lines: 43500000 Finished processing child process. Exiting.. Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 44000000 Processed lines: 44000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Processed lines: 44000000 Finished processing child process. Exiting.. Processed lines: 44000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 44096319 lines in total Total number of methylation call strings processed: 88192638 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1036370828 Total methylated C's in CpG context: 13257071 Total methylated C's in CHG context: 856075 Total methylated C's in CHH context: 3718164 Total C to T conversions in CpG context: 118387681 Total C to T conversions in CHG context: 177358593 Total C to T conversions in CHH context: 722793244 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.21.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -p 8 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz -2 /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz" Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 500000 Processed lines: 1000000 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lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 11000000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 10500000 Processed lines: 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lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 13000000 Processed lines: 12500000 Processed lines: 12500000 Processed lines: 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Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 15000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 13500000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14000000 Processed lines: 14500000 Processed 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Processed lines: 37000000 Processed lines: 34000000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34500000 Processed lines: 33500000 Processed lines: 33500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34000000 Processed lines: 37500000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34000000 Finished processing child process. Exiting.. Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 34500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 35500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Processed lines: 36500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 36500000 Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 37500000 Processed lines: 36500000 Processed lines: 36500000 Finished processing child process. Exiting.. Processed lines: 36500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Finished processing child process. Exiting.. Processed lines: 37000000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37000000 Finished processing child process. Exiting.. Processed lines: 37000000 Processed lines: 37000000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Finished processing child process. Exiting.. Finished processing child process. Exiting.. Processed lines: 37500000 Processed lines: 37500000 Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 37592253 lines in total Total number of methylation call strings processed: 75184506 Final Cytosine Methylation Report ================================= Total number of C's analysed: 903220750 Total methylated C's in CpG context: 11490959 Total methylated C's in CHG context: 711903 Total methylated C's in CHH context: 3019557 Total C to T conversions in CpG context: 105465948 Total C to T conversions in CHG context: 157214343 Total C to T conversions in CHH context: 625318040 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/030521-ronrosM/CpG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 10 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr3534_10_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_10_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_10_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_1_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_1_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_1_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_2_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_2_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_2_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_3_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_3_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_3_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_4_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_4_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_4_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_5_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_5_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_5_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_6_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_6_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_6_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_7_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_7_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_7_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_8_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_8_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_8_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_9_R1.fastp-trim.20201202_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_9_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt < Processing alignment report zr3534_9_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 10 Bismark BAM file(s)... >> Reading from Bismark report: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/sr320/030521-ronrosM [INFO ] bismark : Found 10 bismark alignment reports [INFO ] bismark : Found 10 bismark dedup reports [INFO ] bismark : Found 10 bismark methextract reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... [bam_sort_core] merging from 28 files and 28 in-memory blocks... Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_10_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 817 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1826213 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1967257 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1856998 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1606199 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1935987 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1908957 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1932732 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1725591 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1105718 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1765597 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3224 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 29113 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 2539 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 3026 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2490 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15549 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2129 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2877 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2048 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3175 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2016 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 32626 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2589 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2541 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2392 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1307 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 18158 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1344 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 2122 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2619 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2197 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 16689 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1218 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1463 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 716 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1216 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 18259 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1658 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1056 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1328 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1102 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1336 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 18936 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 766 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 872 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 344 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 13507 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1498 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 730 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 399 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 16175 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 239 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 13501 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 24616 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 110 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 16343 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 11690 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12675 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 15407 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4131 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 6615 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8989 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4339 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1457 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 6897 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10163 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12041 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13012 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 10662 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 11486 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 8882 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 10638 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 11864 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11938 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 10125 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 14093 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 10719 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 8483 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 8999 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 8555 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 20485 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6179 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7506 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 5013 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 23308 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 5738 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 15818 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 6127 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 11840 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3015 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 3864 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 4283 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7443 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 5352 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5040 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 6039 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5021 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 4748 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 4832 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 21449 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2698 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 74988 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3865 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4509 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4703 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4314 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 22875 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 7195 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 4084 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3809 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4906 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3776 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4117 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9716 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3620 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4230 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4949 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 10593 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4565 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3121 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 3013 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 3328 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17424 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3821 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2909 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2489 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5009 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2796 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1747 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3583 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3366 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 18115 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 1914 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 16258 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1331 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4433 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4076 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3671 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 6105 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1212 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5306 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2658 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1008 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1231 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1228 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2494 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1462 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2060 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2341 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 854 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1833 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1892 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2358 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 967 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 11633 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6600 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1371 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 9467 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2906 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2105 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3609 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3379 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 651 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5113 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1647 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1522 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1423 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4195 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3011 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1604 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6686 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2577 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10187 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 15870 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 6983 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10291 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 4911 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 289 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 528 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 9004 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 9624 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22629 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 8779 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1092 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 22363 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3566 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 955 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6335 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7216 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 499 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3493 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 15126 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 14233 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6180 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5247 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1524 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3816 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5733 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6563 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 11072 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6781 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1489 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 15170 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2230 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2333 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 8837 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 680 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 912 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6374 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1796 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1585 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2471 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1090 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3602 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5366 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2373 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 226 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 577 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5193 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3311 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 167 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6192 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 3833 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10622 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 682 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4697 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1598 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7358 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2748 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 4685 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 668 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2207 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3171 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8814 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1435 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_10_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_10_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_1_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 818 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1791652 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1859120 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1823614 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1575846 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1863356 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1879249 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1910085 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1653488 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1041612 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1763012 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3630 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 26710 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3501 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 2444 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2346 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 14549 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 1892 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2398 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2180 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3459 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2099 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 28690 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2075 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2480 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 1998 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1429 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 17133 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1590 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1989 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 1363 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2334 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 17689 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1278 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1428 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 705 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1081 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 16185 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1697 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1091 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1118 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 799 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1314 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 18011 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 565 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 792 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 827 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 13506 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1482 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 733 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 645 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 16509 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 195 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 13502 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 20571 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 15658 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 11912 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12199 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 13719 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 3566 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 8988 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8124 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4740 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1621 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 4774 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 9723 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12380 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 12844 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 7695 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 9749 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10420 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11601 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12600 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11175 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 12352 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 13915 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 10921 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 10513 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 8748 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 9026 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 21938 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6892 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7971 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 4476 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 24443 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 4474 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 11426 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5510 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 9804 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3052 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 4553 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 4808 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7361 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 8107 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 4912 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 6597 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 4643 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5686 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 4791 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 22844 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2846 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 74516 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 4657 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4157 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 3394 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 3996 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 22479 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 5168 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3322 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 2835 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 2664 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 4186 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4442 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9857 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3650 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4020 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4422 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 12765 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 3979 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 4243 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 4897 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 2685 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 16541 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 4351 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2749 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2585 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5169 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2583 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1712 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3252 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3835 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 17098 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 1730 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15360 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1487 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4397 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4402 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3696 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 5002 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1246 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5164 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 3002 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1055 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1666 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 979 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2608 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1401 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2075 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 839 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 897 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1571 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1885 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2361 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 996 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 11749 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6431 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1384 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 8971 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2693 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 1984 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 2907 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3414 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 2145 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 4951 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1664 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1529 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3624 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 3944 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3066 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1609 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6615 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2557 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 9589 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 15071 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7043 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10744 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6284 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 366 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 629 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 7712 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8110 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22831 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 9626 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1223 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 21003 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3590 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 947 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6410 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7249 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 617 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3529 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 14878 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 12909 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6299 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5291 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1469 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3840 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5564 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6796 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10542 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6323 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1481 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 14687 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2206 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2327 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9420 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 673 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 898 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6323 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 3156 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1612 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2335 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1130 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3292 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5222 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2439 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 244 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 610 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5139 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3171 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 268 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6393 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4058 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10356 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 692 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4664 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1591 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7551 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2799 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5491 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 716 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2186 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3077 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8470 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1346 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_1_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_1_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_2_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 805 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1793907 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1869961 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1825568 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1564135 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1909704 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1871662 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1906469 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1654858 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1052465 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1753887 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3617 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 26172 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3407 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 2119 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2644 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15063 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 1908 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2679 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2171 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3622 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2072 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 28650 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2140 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2660 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2284 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1225 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 17528 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1080 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1761 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2437 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2280 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 14708 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1332 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1663 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 589 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1108 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 15350 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1687 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1067 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1252 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1039 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1395 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 15851 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 810 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 525 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 810 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 12479 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1532 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 755 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 414 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 11124 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 267 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 12723 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 18911 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 1 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 13772 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 10462 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 11811 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 13693 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4263 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 7936 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8035 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4410 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1925 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 8265 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10123 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 10335 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 12462 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 10294 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 10021 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 9767 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11212 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12411 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 12189 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 11714 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 13896 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 9279 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 9004 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 8929 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 9545 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 20125 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6947 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7848 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 4586 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 24040 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 5589 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 13299 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5015 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 11780 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 2940 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 7047 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 3723 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7235 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 7872 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5569 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 5077 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 4903 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5119 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 4636 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 19707 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2450 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 70744 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3782 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 3480 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 3565 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4081 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 23293 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 4579 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3483 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3474 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 5233 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3646 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4298 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 10291 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3496 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4177 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4845 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 12898 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4531 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3637 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 5528 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 2673 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17190 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 4436 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2651 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2319 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5602 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2069 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1987 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 2760 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3955 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 16909 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 4438 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15252 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 859 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4300 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 3935 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3522 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 4932 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1235 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5702 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2077 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1042 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1141 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 880 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2659 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1418 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2074 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 836 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 541 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1662 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1900 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2363 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 969 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 11414 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6448 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1420 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 9933 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2797 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2102 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3026 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3385 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1955 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5058 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1649 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1510 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 4061 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4160 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3111 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1601 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6608 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2516 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10155 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 15465 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7460 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10402 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 5980 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 386 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1686 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8881 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8060 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 21994 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 9406 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1393 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 20768 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3623 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 922 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6376 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7211 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 507 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3590 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 15047 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13094 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6205 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5335 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1487 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3753 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5866 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6552 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10386 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6683 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1504 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 14594 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2261 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2334 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 8308 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 715 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 929 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6243 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1780 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1628 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2495 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1060 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3548 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5412 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2331 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 239 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 724 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5112 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3207 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 229 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6072 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4006 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10566 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 669 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4692 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1614 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7387 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3066 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 4886 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 524 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2224 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3291 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8795 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1324 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_2_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_2_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_3_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 794 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1813216 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1881310 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1852187 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1600841 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1940334 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1901588 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1939547 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1699074 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1070665 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1781761 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3432 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 24578 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3375 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 1828 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2614 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15369 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2017 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2606 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 1944 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3653 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2184 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 29690 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2144 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2572 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 1861 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1296 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 17792 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1111 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1594 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2415 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 1488 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 15180 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1347 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1633 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 543 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1094 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 15858 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1762 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1097 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1313 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1335 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1428 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 16004 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 822 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 504 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 824 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 12810 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1509 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 797 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 519 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 11279 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 13376 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 21295 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 109 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 14799 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 11052 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 11802 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 13821 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 3703 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 8070 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8169 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4437 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 2049 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 8657 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10350 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 10574 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13007 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 10580 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 10333 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10384 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11462 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12612 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 13092 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 11900 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 14037 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 8456 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 9481 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9175 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 9607 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 20073 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 7137 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7822 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 5129 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 24514 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 4509 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 19428 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5208 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 9102 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3436 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 4728 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 7370 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7343 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 8214 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5879 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 5128 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5040 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 4951 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 4708 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 20918 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2728 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 78376 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3917 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 3325 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 3645 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4471 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 23785 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 4444 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3493 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3571 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 5384 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3765 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4285 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9679 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3575 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4361 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4714 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 12942 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4034 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3741 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 5561 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 2728 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17246 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 4490 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2892 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2456 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5501 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2171 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1973 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 2716 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3975 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 17104 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 4135 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15317 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1235 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4423 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4373 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3582 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 5066 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1257 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5721 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2127 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1035 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 936 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1168 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2621 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1444 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2091 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 794 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 517 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 2964 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1971 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2537 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 995 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 12918 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6507 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1419 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 10302 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2843 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2142 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3085 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3408 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1933 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5013 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1675 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1480 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3704 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4220 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3112 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1622 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6420 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2575 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 9638 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 15480 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7507 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10530 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6111 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 395 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1730 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 7825 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8598 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22478 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 9637 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1383 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 21233 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3662 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 933 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6488 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7288 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 511 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3558 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 15180 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13379 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6448 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5352 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1456 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3801 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5631 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6549 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 11238 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6776 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1482 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 14343 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2285 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2366 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9402 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 726 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 942 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6363 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1832 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1623 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2537 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1095 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3600 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5512 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2369 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 237 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 723 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 4989 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3221 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 242 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6134 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4068 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10750 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 714 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4666 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1573 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7453 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2941 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5653 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 580 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2228 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3179 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8840 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1347 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_3_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_3_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_4_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 815 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1790384 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1883254 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1820583 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1558345 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1883000 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1864103 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1903341 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1656422 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1064399 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1746364 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3411 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 25955 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3062 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 2908 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2630 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 13474 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2160 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2742 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2066 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 1759 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 1945 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 28509 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2694 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2428 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2217 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1141 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 17597 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1350 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 2225 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 1622 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 1591 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 16493 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1236 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1857 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 639 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1093 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 15283 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1675 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1044 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1288 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1110 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1409 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 14906 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 610 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 640 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 619 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 12890 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1513 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 675 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 893 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 12152 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 144 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 12486 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 19622 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 113 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 14727 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 12798 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12893 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 14742 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4256 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 7769 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8982 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4672 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 2049 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 5773 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10478 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 11742 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13275 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 9360 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 11241 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 9292 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11837 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12239 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11380 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 10712 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 12173 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 9355 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 8802 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9013 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 8109 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 21909 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6689 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 8208 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 4963 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 23408 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 6198 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 14804 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5509 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 8898 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3118 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 4594 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 3573 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 6766 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 5513 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 4894 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 6270 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5860 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5739 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 5353 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 21599 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 3247 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 74694 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3245 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4402 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4993 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4106 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 23338 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 6484 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 4146 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3845 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4444 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3530 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 1871 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9738 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3599 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4268 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4418 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 10061 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 3847 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3257 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2720 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 3324 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17933 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3442 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2853 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 3040 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 4929 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2806 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1752 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3018 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3132 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 18854 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 3517 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 14777 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1214 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4366 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 3592 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3508 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 5819 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1227 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5400 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2310 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1024 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1482 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 1276 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2546 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1470 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2072 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2123 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 517 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1036 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1927 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2505 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 979 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 7979 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6313 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1428 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 9539 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2764 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 1957 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 2852 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3359 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1884 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5069 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1651 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1488 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1350 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4075 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3054 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1622 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6563 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2564 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 9560 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 16696 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 6885 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10582 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6799 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 344 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1365 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8757 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8411 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22801 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 10881 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1456 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 21201 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3536 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 960 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6418 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7188 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 691 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3508 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 14934 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 12851 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6335 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5293 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1489 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3802 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5808 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6727 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10405 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6868 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1481 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 14720 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2288 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2326 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9435 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 656 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 914 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6290 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1849 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1635 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2421 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1047 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3784 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5182 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2477 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 234 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 2294 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5218 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3229 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 204 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6505 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4071 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10377 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 699 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4558 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1601 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7553 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2876 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 4863 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 733 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2276 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3223 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8646 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1277 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 236 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994818.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_4_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_4_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_5_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 804 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1812335 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1870161 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1851338 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1590597 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1925385 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1894163 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1924858 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1674819 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1070760 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1772366 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3396 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 24352 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3204 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 4416 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 3478 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 16224 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2200 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2445 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2170 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3428 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2131 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 29601 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 1957 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2642 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2125 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1258 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 17871 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1664 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1532 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2881 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 1574 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 15590 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1344 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 2187 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 665 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1163 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 15745 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1630 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1110 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1272 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1060 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1421 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 18451 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 941 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 484 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 349 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 16127 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1474 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 829 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 867 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 13610 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 178 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 14429 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 18871 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 108 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 4 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 16611 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 12033 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12184 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 18848 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4448 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 9680 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8433 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4132 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1678 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 7435 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 11191 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12101 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 11649 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 9999 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 12427 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10869 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 10404 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 11858 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 12178 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 9823 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 14182 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 10456 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 10076 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9148 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 8020 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 22255 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 8167 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 6984 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 5148 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 24642 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 5937 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 15290 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5802 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 12909 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3143 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 4937 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 4292 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7403 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 5702 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 4786 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 6765 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5575 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5285 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 6997 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 22793 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 3023 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 87492 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 4848 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4200 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4922 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4864 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 22195 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 7140 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3508 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3811 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4394 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3862 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 1928 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9163 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 4363 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4066 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4195 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 11291 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 3490 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3061 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2375 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 4831 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 18276 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3267 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2728 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2261 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5404 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 3173 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1995 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3077 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3483 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 18612 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 1661 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 16341 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 2140 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4404 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4314 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3741 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 4967 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1236 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5322 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2852 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1024 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1605 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 870 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2556 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1397 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2026 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 827 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 831 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1263 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1961 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2487 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 968 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 11143 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6488 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1376 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 9257 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2903 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2062 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 2999 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3383 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 645 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5136 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1655 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1483 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1488 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 3828 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3083 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1624 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6669 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2534 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10545 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 16358 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7681 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10422 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6959 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 304 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 547 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8070 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8532 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22579 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 11805 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2126 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 22273 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3629 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 910 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6443 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7170 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 603 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3709 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 14636 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 12949 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6278 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5336 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1634 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3737 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5716 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6768 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10869 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6417 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1488 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 15431 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2168 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2350 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9641 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 685 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 927 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6307 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1834 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1616 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2505 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1076 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3589 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5227 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2322 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 247 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 1028 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5260 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3382 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 247 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6101 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4110 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10717 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 693 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4678 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1603 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7376 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3430 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 4838 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 718 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2253 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3112 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8920 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1432 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_5_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_5_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_6_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 823 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1830597 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1957970 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1876424 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1610575 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1981450 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1934206 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1945702 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1712970 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1123444 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1799760 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 1240 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 25231 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 2872 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 1994 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 3730 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 18115 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2061 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2581 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2084 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3335 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2192 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 29697 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2260 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2693 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2526 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1265 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 18429 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1074 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 2098 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2611 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2132 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 17936 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1597 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1540 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 561 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1171 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 17930 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1575 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1109 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1271 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1047 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1272 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 15540 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 858 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 764 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 383 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 14308 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1482 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 753 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 959 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 16738 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 358 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 14646 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 24371 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 112 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 2 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 15611 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 13215 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12952 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 16407 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4629 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 6462 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 9535 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 2650 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1801 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 5299 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 11201 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12752 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13077 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 10338 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 12526 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10725 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11213 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 13097 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11196 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 10473 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 15091 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 8217 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 9421 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9281 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 9508 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 21605 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6915 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 8587 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 10612 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 23386 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 5633 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 14791 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5590 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 9946 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 4194 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 3558 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 3832 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 6527 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 8136 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5889 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 4832 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5229 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 4664 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 5221 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 21403 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 3210 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 81568 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3680 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4151 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4553 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4295 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 22692 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 7212 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3671 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 3822 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 5385 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3825 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 3934 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 7746 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3787 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 3670 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4582 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 12751 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4368 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 4370 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2182 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 3919 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 19446 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 5210 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2613 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2834 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5314 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2501 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1978 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3729 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3452 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 17619 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 3408 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15668 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 763 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4519 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 3947 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3652 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 6819 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1260 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5541 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2780 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1034 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1393 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 898 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2633 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1481 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2131 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2755 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 834 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1686 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1972 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2584 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 970 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 9607 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6689 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1385 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 8828 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2841 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2170 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3127 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3380 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 2097 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5131 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1701 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1538 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1375 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4300 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3065 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1624 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6736 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2589 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10475 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 16766 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7267 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10889 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6173 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 395 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 654 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8742 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8245 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22901 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 8731 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 2159 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 21607 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3562 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 997 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6367 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7393 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 525 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3642 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 15108 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13882 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6431 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5340 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1561 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3877 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5850 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6812 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10719 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 7013 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1470 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 15198 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2255 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2458 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9370 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 728 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 943 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6559 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1851 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1650 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2512 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1052 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3482 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5490 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2425 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 251 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 514 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5384 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3255 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 222 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6201 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4006 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10789 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 722 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4739 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1606 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7463 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2944 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5734 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 718 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2212 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3260 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8791 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1445 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_6_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_6_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_7_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 822 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1808525 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1904123 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1845183 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1560519 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1901861 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1882703 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1916452 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1662326 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1096249 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1764314 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 2991 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 26835 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 2994 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 1866 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2359 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15674 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2111 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2720 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2046 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 1566 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 2006 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 30298 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 1913 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2714 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 1956 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1213 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 18801 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1252 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1742 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2440 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 1975 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 16816 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1634 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1105 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 467 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1163 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 15474 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1621 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 999 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1186 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 750 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1307 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 14476 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 783 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 592 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 656 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 12974 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1454 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 801 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 477 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 13863 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 182 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 13245 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 20289 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 111 different covered positions) Writing cytosine report for chromosome NW_022994818.1 (stored 3 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 14321 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 12521 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 12914 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 14975 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4008 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 7837 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8863 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4325 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1930 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 6518 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10071 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 11265 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13101 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 8961 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 11315 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10078 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 11349 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 11660 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 10745 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 9444 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 12952 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 10403 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 8812 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 8956 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 8266 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 20988 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6513 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 8034 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 4750 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 23681 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 6258 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 14007 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5734 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 11091 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 2848 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 3638 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 7034 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 6787 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 4946 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5332 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 5342 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5687 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 4570 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 5486 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 22184 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2858 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 66859 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3855 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4106 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4616 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 3961 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 21168 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 5933 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 3884 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 4300 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4234 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3649 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4544 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9683 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3588 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4082 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4142 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 9805 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4487 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3366 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2976 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 3619 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17022 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3326 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2706 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 2811 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5135 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2850 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1627 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3278 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3606 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 17821 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 3235 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15924 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1015 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4375 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4050 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3624 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 6662 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1218 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5574 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2624 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1017 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1696 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 870 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2612 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1449 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2075 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 1852 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 540 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1363 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1902 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2498 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 948 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 9081 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6567 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1388 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 8712 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2830 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 1982 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 2995 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3368 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1737 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5115 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1678 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1409 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1349 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4142 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3044 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1582 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6608 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2497 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10172 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 16198 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7380 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10293 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 6779 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 687 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 495 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8511 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 9071 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22550 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 10772 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1813 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 22004 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3547 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 943 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6481 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7207 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 622 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3538 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 14802 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13359 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6314 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5314 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1540 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3680 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5863 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6659 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10815 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6308 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1475 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 15090 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2242 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2342 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 8990 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 690 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 914 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6280 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1811 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1612 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2470 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1066 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3290 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5161 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2295 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 251 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 737 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5108 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3357 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 186 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6061 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 3897 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10334 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 708 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4726 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1581 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7554 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3033 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5416 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 731 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2232 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3147 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8704 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1356 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 237 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_7_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_7_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_8_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 806 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1863781 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 2028568 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1912082 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1633027 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 2012433 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1953347 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1983635 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1748018 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1134846 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1826668 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3850 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 29136 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 3028 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 3242 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2723 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15922 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2257 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2787 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 2145 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3416 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 1777 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 34007 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2248 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2553 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 2737 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1232 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 19983 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1250 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 2141 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2606 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2417 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 18130 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1317 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1710 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 755 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1285 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 17207 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1700 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1102 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1318 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1255 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1366 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 15793 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 820 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 674 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 316 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 13558 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1504 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 838 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 918 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 13046 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 213 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 14615 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 25606 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 116 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 15602 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 12364 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 13002 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 18280 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4631 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 8869 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 9234 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 4460 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1949 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 7438 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 11142 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12940 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13541 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 9316 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 11559 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 10293 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 10414 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12532 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11851 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 10158 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 14011 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 9759 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 10126 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9223 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 7722 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 27604 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6809 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7866 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 5723 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 23238 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 6251 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 18680 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 5638 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 11698 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 3248 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 5135 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 4211 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7878 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 5429 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5101 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 5214 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5408 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5386 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 5291 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 24402 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 3238 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 82027 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 3932 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 4498 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4619 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4840 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 21903 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 6835 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 4198 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 4249 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4817 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3449 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 4230 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 7328 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 4481 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4471 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4414 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 11102 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4825 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3725 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2762 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 2622 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 18497 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3397 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2927 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 3214 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5524 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2775 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 2180 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3646 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 3791 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 19109 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 2089 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 16795 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 2142 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4593 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4502 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3747 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 6910 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1234 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5627 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2222 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1051 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1966 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 868 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2613 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1477 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2147 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2147 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 906 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 2238 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1926 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2377 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 976 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 11776 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6531 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1412 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 9534 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2913 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 2171 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3141 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3400 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 722 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5306 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1721 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1446 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 1453 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 3877 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3123 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1613 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6947 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2545 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 10045 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 15991 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7532 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 11099 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 5041 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 377 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 2114 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 8611 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 9303 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 21972 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 9965 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1761 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 21561 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3619 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 1052 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6466 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7310 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 546 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3601 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 15165 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13525 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6502 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5467 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1535 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3793 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5870 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6639 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 11353 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6872 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1477 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 15028 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2219 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2413 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9270 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 698 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 958 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6553 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1933 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1652 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2551 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1070 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 4019 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5278 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2356 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 253 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 789 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5386 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3403 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 245 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6233 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4212 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10665 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 704 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4647 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1608 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7635 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 3096 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5658 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 741 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2273 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3236 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8745 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1488 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 236 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994818.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_8_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_8_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq! Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/030521-ronrosM/< Genome directory: >/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/< CX context: no (CpG context only, default) Pooling CpG top/bottom strand evidence: yes Genome coordinates used: 0-based (user specified) GZIP compression: no Split by chromosome: no Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Stored sequence information of 237 chromosomes/scaffolds in total ============================================================================== Methylation information will now be written into a genome-wide cytosine report ============================================================================== >>> Writing genome-wide cytosine report to: zr3534_9_R1.fastp-trim.20201202.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_001276.1 Writing cytosine report for chromosome NC_001276.1 (stored 806 different covered positions) Writing cytosine report for chromosome NC_047559.1 (stored 1810210 different covered positions) Writing cytosine report for chromosome NC_047560.1 (stored 1929089 different covered positions) Writing cytosine report for chromosome NC_047561.1 (stored 1862288 different covered positions) Writing cytosine report for chromosome NC_047562.1 (stored 1580199 different covered positions) Writing cytosine report for chromosome NC_047563.1 (stored 1920536 different covered positions) Writing cytosine report for chromosome NC_047564.1 (stored 1903647 different covered positions) Writing cytosine report for chromosome NC_047565.1 (stored 1921901 different covered positions) Writing cytosine report for chromosome NC_047566.1 (stored 1697218 different covered positions) Writing cytosine report for chromosome NC_047567.1 (stored 1070112 different covered positions) Writing cytosine report for chromosome NC_047568.1 (stored 1773691 different covered positions) Writing cytosine report for chromosome NW_022994773.1 (stored 3030 different covered positions) Writing cytosine report for chromosome NW_022994774.1 (stored 28908 different covered positions) Writing cytosine report for chromosome NW_022994775.1 (stored 2499 different covered positions) Writing cytosine report for chromosome NW_022994776.1 (stored 1586 different covered positions) Writing cytosine report for chromosome NW_022994777.1 (stored 2373 different covered positions) Writing cytosine report for chromosome NW_022994778.1 (stored 15617 different covered positions) Writing cytosine report for chromosome NW_022994779.1 (stored 2112 different covered positions) Writing cytosine report for chromosome NW_022994780.1 (stored 2543 different covered positions) Writing cytosine report for chromosome NW_022994781.1 (stored 1978 different covered positions) Writing cytosine report for chromosome NW_022994782.1 (stored 3317 different covered positions) Writing cytosine report for chromosome NW_022994783.1 (stored 1957 different covered positions) Writing cytosine report for chromosome NW_022994784.1 (stored 29763 different covered positions) Writing cytosine report for chromosome NW_022994785.1 (stored 2123 different covered positions) Writing cytosine report for chromosome NW_022994786.1 (stored 2575 different covered positions) Writing cytosine report for chromosome NW_022994787.1 (stored 1755 different covered positions) Writing cytosine report for chromosome NW_022994788.1 (stored 1303 different covered positions) Writing cytosine report for chromosome NW_022994789.1 (stored 18240 different covered positions) Writing cytosine report for chromosome NW_022994790.1 (stored 1283 different covered positions) Writing cytosine report for chromosome NW_022994791.1 (stored 1746 different covered positions) Writing cytosine report for chromosome NW_022994792.1 (stored 2568 different covered positions) Writing cytosine report for chromosome NW_022994793.1 (stored 2431 different covered positions) Writing cytosine report for chromosome NW_022994794.1 (stored 17247 different covered positions) Writing cytosine report for chromosome NW_022994795.1 (stored 1604 different covered positions) Writing cytosine report for chromosome NW_022994796.1 (stored 1220 different covered positions) Writing cytosine report for chromosome NW_022994797.1 (stored 501 different covered positions) Writing cytosine report for chromosome NW_022994798.1 (stored 1157 different covered positions) Writing cytosine report for chromosome NW_022994799.1 (stored 17402 different covered positions) Writing cytosine report for chromosome NW_022994800.1 (stored 1609 different covered positions) Writing cytosine report for chromosome NW_022994801.1 (stored 1069 different covered positions) Writing cytosine report for chromosome NW_022994802.1 (stored 1260 different covered positions) Writing cytosine report for chromosome NW_022994803.1 (stored 1037 different covered positions) Writing cytosine report for chromosome NW_022994804.1 (stored 1455 different covered positions) Writing cytosine report for chromosome NW_022994805.1 (stored 15384 different covered positions) Writing cytosine report for chromosome NW_022994806.1 (stored 747 different covered positions) Writing cytosine report for chromosome NW_022994807.1 (stored 862 different covered positions) Writing cytosine report for chromosome NW_022994808.1 (stored 580 different covered positions) Writing cytosine report for chromosome NW_022994809.1 (stored 14603 different covered positions) Writing cytosine report for chromosome NW_022994810.1 (stored 1495 different covered positions) Writing cytosine report for chromosome NW_022994811.1 (stored 759 different covered positions) Writing cytosine report for chromosome NW_022994812.1 (stored 487 different covered positions) Writing cytosine report for chromosome NW_022994813.1 (stored 17846 different covered positions) Writing cytosine report for chromosome NW_022994814.1 (stored 132 different covered positions) Writing cytosine report for chromosome NW_022994815.1 (stored 13812 different covered positions) Writing cytosine report for chromosome NW_022994816.1 (stored 24406 different covered positions) Writing cytosine report for chromosome NW_022994817.1 (stored 107 different covered positions) Writing cytosine report for chromosome NW_022994819.1 (stored 16305 different covered positions) Writing cytosine report for chromosome NW_022994820.1 (stored 12593 different covered positions) Writing cytosine report for chromosome NW_022994821.1 (stored 13363 different covered positions) Writing cytosine report for chromosome NW_022994822.1 (stored 17822 different covered positions) Writing cytosine report for chromosome NW_022994823.1 (stored 4586 different covered positions) Writing cytosine report for chromosome NW_022994824.1 (stored 7477 different covered positions) Writing cytosine report for chromosome NW_022994825.1 (stored 8952 different covered positions) Writing cytosine report for chromosome NW_022994826.1 (stored 3573 different covered positions) Writing cytosine report for chromosome NW_022994827.1 (stored 1610 different covered positions) Writing cytosine report for chromosome NW_022994828.1 (stored 6023 different covered positions) Writing cytosine report for chromosome NW_022994829.1 (stored 10092 different covered positions) Writing cytosine report for chromosome NW_022994830.1 (stored 12114 different covered positions) Writing cytosine report for chromosome NW_022994831.1 (stored 13358 different covered positions) Writing cytosine report for chromosome NW_022994832.1 (stored 11856 different covered positions) Writing cytosine report for chromosome NW_022994833.1 (stored 11865 different covered positions) Writing cytosine report for chromosome NW_022994834.1 (stored 8840 different covered positions) Writing cytosine report for chromosome NW_022994835.1 (stored 10855 different covered positions) Writing cytosine report for chromosome NW_022994836.1 (stored 12464 different covered positions) Writing cytosine report for chromosome NW_022994837.1 (stored 11352 different covered positions) Writing cytosine report for chromosome NW_022994838.1 (stored 10087 different covered positions) Writing cytosine report for chromosome NW_022994839.1 (stored 14127 different covered positions) Writing cytosine report for chromosome NW_022994840.1 (stored 10619 different covered positions) Writing cytosine report for chromosome NW_022994841.1 (stored 8898 different covered positions) Writing cytosine report for chromosome NW_022994842.1 (stored 9019 different covered positions) Writing cytosine report for chromosome NW_022994843.1 (stored 7998 different covered positions) Writing cytosine report for chromosome NW_022994844.1 (stored 20259 different covered positions) Writing cytosine report for chromosome NW_022994845.1 (stored 6767 different covered positions) Writing cytosine report for chromosome NW_022994846.1 (stored 7773 different covered positions) Writing cytosine report for chromosome NW_022994847.1 (stored 4854 different covered positions) Writing cytosine report for chromosome NW_022994848.1 (stored 24177 different covered positions) Writing cytosine report for chromosome NW_022994849.1 (stored 5682 different covered positions) Writing cytosine report for chromosome NW_022994850.1 (stored 16480 different covered positions) Writing cytosine report for chromosome NW_022994851.1 (stored 6113 different covered positions) Writing cytosine report for chromosome NW_022994852.1 (stored 10945 different covered positions) Writing cytosine report for chromosome NW_022994853.1 (stored 2888 different covered positions) Writing cytosine report for chromosome NW_022994854.1 (stored 3429 different covered positions) Writing cytosine report for chromosome NW_022994855.1 (stored 3704 different covered positions) Writing cytosine report for chromosome NW_022994856.1 (stored 7484 different covered positions) Writing cytosine report for chromosome NW_022994857.1 (stored 5321 different covered positions) Writing cytosine report for chromosome NW_022994858.1 (stored 5153 different covered positions) Writing cytosine report for chromosome NW_022994859.1 (stored 5367 different covered positions) Writing cytosine report for chromosome NW_022994860.1 (stored 5211 different covered positions) Writing cytosine report for chromosome NW_022994861.1 (stored 5018 different covered positions) Writing cytosine report for chromosome NW_022994862.1 (stored 5137 different covered positions) Writing cytosine report for chromosome NW_022994863.1 (stored 22040 different covered positions) Writing cytosine report for chromosome NW_022994864.1 (stored 2852 different covered positions) Writing cytosine report for chromosome NW_022994865.1 (stored 66766 different covered positions) Writing cytosine report for chromosome NW_022994866.1 (stored 4002 different covered positions) Writing cytosine report for chromosome NW_022994867.1 (stored 3739 different covered positions) Writing cytosine report for chromosome NW_022994868.1 (stored 4834 different covered positions) Writing cytosine report for chromosome NW_022994869.1 (stored 4625 different covered positions) Writing cytosine report for chromosome NW_022994870.1 (stored 19995 different covered positions) Writing cytosine report for chromosome NW_022994871.1 (stored 6713 different covered positions) Writing cytosine report for chromosome NW_022994872.1 (stored 4231 different covered positions) Writing cytosine report for chromosome NW_022994873.1 (stored 4034 different covered positions) Writing cytosine report for chromosome NW_022994874.1 (stored 4316 different covered positions) Writing cytosine report for chromosome NW_022994875.1 (stored 3869 different covered positions) Writing cytosine report for chromosome NW_022994876.1 (stored 2561 different covered positions) Writing cytosine report for chromosome NW_022994877.1 (stored 9574 different covered positions) Writing cytosine report for chromosome NW_022994878.1 (stored 3479 different covered positions) Writing cytosine report for chromosome NW_022994879.1 (stored 4280 different covered positions) Writing cytosine report for chromosome NW_022994880.1 (stored 4732 different covered positions) Writing cytosine report for chromosome NW_022994881.1 (stored 10596 different covered positions) Writing cytosine report for chromosome NW_022994882.1 (stored 4380 different covered positions) Writing cytosine report for chromosome NW_022994883.1 (stored 3184 different covered positions) Writing cytosine report for chromosome NW_022994884.1 (stored 2967 different covered positions) Writing cytosine report for chromosome NW_022994885.1 (stored 4582 different covered positions) Writing cytosine report for chromosome NW_022994886.1 (stored 17698 different covered positions) Writing cytosine report for chromosome NW_022994887.1 (stored 3488 different covered positions) Writing cytosine report for chromosome NW_022994888.1 (stored 2750 different covered positions) Writing cytosine report for chromosome NW_022994889.1 (stored 3119 different covered positions) Writing cytosine report for chromosome NW_022994890.1 (stored 5287 different covered positions) Writing cytosine report for chromosome NW_022994891.1 (stored 2910 different covered positions) Writing cytosine report for chromosome NW_022994892.1 (stored 1867 different covered positions) Writing cytosine report for chromosome NW_022994893.1 (stored 3750 different covered positions) Writing cytosine report for chromosome NW_022994894.1 (stored 2754 different covered positions) Writing cytosine report for chromosome NW_022994895.1 (stored 17951 different covered positions) Writing cytosine report for chromosome NW_022994896.1 (stored 3270 different covered positions) Writing cytosine report for chromosome NW_022994897.1 (stored 15241 different covered positions) Writing cytosine report for chromosome NW_022994898.1 (stored 1434 different covered positions) Writing cytosine report for chromosome NW_022994899.1 (stored 4392 different covered positions) Writing cytosine report for chromosome NW_022994900.1 (stored 4198 different covered positions) Writing cytosine report for chromosome NW_022994901.1 (stored 3584 different covered positions) Writing cytosine report for chromosome NW_022994902.1 (stored 6240 different covered positions) Writing cytosine report for chromosome NW_022994903.1 (stored 1227 different covered positions) Writing cytosine report for chromosome NW_022994904.1 (stored 5487 different covered positions) Writing cytosine report for chromosome NW_022994905.1 (stored 2714 different covered positions) Writing cytosine report for chromosome NW_022994906.1 (stored 1008 different covered positions) Writing cytosine report for chromosome NW_022994907.1 (stored 1199 different covered positions) Writing cytosine report for chromosome NW_022994908.1 (stored 954 different covered positions) Writing cytosine report for chromosome NW_022994909.1 (stored 2706 different covered positions) Writing cytosine report for chromosome NW_022994910.1 (stored 1438 different covered positions) Writing cytosine report for chromosome NW_022994911.1 (stored 2093 different covered positions) Writing cytosine report for chromosome NW_022994912.1 (stored 2172 different covered positions) Writing cytosine report for chromosome NW_022994913.1 (stored 853 different covered positions) Writing cytosine report for chromosome NW_022994914.1 (stored 1097 different covered positions) Writing cytosine report for chromosome NW_022994915.1 (stored 1902 different covered positions) Writing cytosine report for chromosome NW_022994916.1 (stored 2342 different covered positions) Writing cytosine report for chromosome NW_022994917.1 (stored 964 different covered positions) Writing cytosine report for chromosome NW_022994918.1 (stored 9077 different covered positions) Writing cytosine report for chromosome NW_022994919.1 (stored 6621 different covered positions) Writing cytosine report for chromosome NW_022994920.1 (stored 1372 different covered positions) Writing cytosine report for chromosome NW_022994921.1 (stored 8976 different covered positions) Writing cytosine report for chromosome NW_022994922.1 (stored 2840 different covered positions) Writing cytosine report for chromosome NW_022994923.1 (stored 1907 different covered positions) Writing cytosine report for chromosome NW_022994924.1 (stored 3020 different covered positions) Writing cytosine report for chromosome NW_022994925.1 (stored 3335 different covered positions) Writing cytosine report for chromosome NW_022994926.1 (stored 1681 different covered positions) Writing cytosine report for chromosome NW_022994927.1 (stored 5138 different covered positions) Writing cytosine report for chromosome NW_022994928.1 (stored 1737 different covered positions) Writing cytosine report for chromosome NW_022994929.1 (stored 1557 different covered positions) Writing cytosine report for chromosome NW_022994930.1 (stored 3246 different covered positions) Writing cytosine report for chromosome NW_022994931.1 (stored 4252 different covered positions) Writing cytosine report for chromosome NW_022994932.1 (stored 3023 different covered positions) Writing cytosine report for chromosome NW_022994933.1 (stored 1612 different covered positions) Writing cytosine report for chromosome NW_022994934.1 (stored 6828 different covered positions) Writing cytosine report for chromosome NW_022994935.1 (stored 2507 different covered positions) Writing cytosine report for chromosome NW_022994936.1 (stored 9568 different covered positions) Writing cytosine report for chromosome NW_022994937.1 (stored 16210 different covered positions) Writing cytosine report for chromosome NW_022994938.1 (stored 7336 different covered positions) Writing cytosine report for chromosome NW_022994939.1 (stored 10785 different covered positions) Writing cytosine report for chromosome NW_022994940.1 (stored 4708 different covered positions) Writing cytosine report for chromosome NW_022994941.1 (stored 673 different covered positions) Writing cytosine report for chromosome NW_022994942.1 (stored 1619 different covered positions) Writing cytosine report for chromosome NW_022994943.1 (stored 7592 different covered positions) Writing cytosine report for chromosome NW_022994944.1 (stored 8702 different covered positions) Writing cytosine report for chromosome NW_022994945.1 (stored 22900 different covered positions) Writing cytosine report for chromosome NW_022994946.1 (stored 10312 different covered positions) Writing cytosine report for chromosome NW_022994947.1 (stored 1978 different covered positions) Writing cytosine report for chromosome NW_022994948.1 (stored 22784 different covered positions) Writing cytosine report for chromosome NW_022994949.1 (stored 3542 different covered positions) Writing cytosine report for chromosome NW_022994950.1 (stored 983 different covered positions) Writing cytosine report for chromosome NW_022994951.1 (stored 6439 different covered positions) Writing cytosine report for chromosome NW_022994952.1 (stored 7256 different covered positions) Writing cytosine report for chromosome NW_022994953.1 (stored 537 different covered positions) Writing cytosine report for chromosome NW_022994954.1 (stored 3588 different covered positions) Writing cytosine report for chromosome NW_022994955.1 (stored 14526 different covered positions) Writing cytosine report for chromosome NW_022994956.1 (stored 13015 different covered positions) Writing cytosine report for chromosome NW_022994957.1 (stored 6322 different covered positions) Writing cytosine report for chromosome NW_022994958.1 (stored 5234 different covered positions) Writing cytosine report for chromosome NW_022994959.1 (stored 1546 different covered positions) Writing cytosine report for chromosome NW_022994960.1 (stored 3638 different covered positions) Writing cytosine report for chromosome NW_022994961.1 (stored 5609 different covered positions) Writing cytosine report for chromosome NW_022994962.1 (stored 6678 different covered positions) Writing cytosine report for chromosome NW_022994963.1 (stored 10806 different covered positions) Writing cytosine report for chromosome NW_022994964.1 (stored 6367 different covered positions) Writing cytosine report for chromosome NW_022994965.1 (stored 1475 different covered positions) Writing cytosine report for chromosome NW_022994966.1 (stored 14953 different covered positions) Writing cytosine report for chromosome NW_022994967.1 (stored 2218 different covered positions) Writing cytosine report for chromosome NW_022994968.1 (stored 2355 different covered positions) Writing cytosine report for chromosome NW_022994969.1 (stored 9431 different covered positions) Writing cytosine report for chromosome NW_022994970.1 (stored 678 different covered positions) Writing cytosine report for chromosome NW_022994971.1 (stored 910 different covered positions) Writing cytosine report for chromosome NW_022994972.1 (stored 6349 different covered positions) Writing cytosine report for chromosome NW_022994973.1 (stored 1879 different covered positions) Writing cytosine report for chromosome NW_022994974.1 (stored 1602 different covered positions) Writing cytosine report for chromosome NW_022994975.1 (stored 2417 different covered positions) Writing cytosine report for chromosome NW_022994976.1 (stored 1088 different covered positions) Writing cytosine report for chromosome NW_022994977.1 (stored 3159 different covered positions) Writing cytosine report for chromosome NW_022994978.1 (stored 5350 different covered positions) Writing cytosine report for chromosome NW_022994979.1 (stored 2382 different covered positions) Writing cytosine report for chromosome NW_022994980.1 (stored 240 different covered positions) Writing cytosine report for chromosome NW_022994981.1 (stored 751 different covered positions) Writing cytosine report for chromosome NW_022994982.1 (stored 5308 different covered positions) Writing cytosine report for chromosome NW_022994983.1 (stored 3268 different covered positions) Writing cytosine report for chromosome NW_022994984.1 (stored 473 different covered positions) Writing cytosine report for chromosome NW_022994985.1 (stored 6070 different covered positions) Writing cytosine report for chromosome NW_022994986.1 (stored 4006 different covered positions) Writing cytosine report for chromosome NW_022994987.1 (stored 10307 different covered positions) Writing cytosine report for chromosome NW_022994988.1 (stored 681 different covered positions) Writing cytosine report for chromosome NW_022994989.1 (stored 4702 different covered positions) Writing cytosine report for chromosome NW_022994990.1 (stored 1616 different covered positions) Writing cytosine report for chromosome NW_022994991.1 (stored 7565 different covered positions) Writing cytosine report for chromosome NW_022994992.1 (stored 2744 different covered positions) Writing cytosine report for chromosome NW_022994993.1 (stored 5433 different covered positions) Writing cytosine report for chromosome NW_022994994.1 (stored 674 different covered positions) Writing cytosine report for chromosome NW_022994995.1 (stored 2263 different covered positions) Writing cytosine report for chromosome NW_022994996.1 (stored 3051 different covered positions) Writing cytosine report for chromosome NW_022994997.1 (stored 8918 different covered positions) Writing cytosine report for last chromosome NW_022994998.1 (stored 1441 different covered positions) Finished writing out cytosine report for covered chromosomes (processed 236 chromosomes/scaffolds in total) Now processing chromosomes that were not covered by any methylation calls in the coverage file... Writing cytosine report for not covered chromosome NW_022994818.1 Finished writing out cytosine report (processed 237 chromosomes/scaffolds in total). coverage2cytosine processing complete. Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>zr3534_9_R1.fastp-trim.20201202.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zr3534_9_R1.fastp-trim.20201202.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!