Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1002'): /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/sr320/analyses/1002 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz to 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz (21462840 sequences in total) Input file is 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/Cvirg-genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-ST0747:461:C64YUACXX:1:1101:1192:2181_1:N:0:TTAGGC 4 * 0 0 * * 0 0 TATATTAAAATTATTTTAATAAAAAATATTTGTTTTATAATAATTATTTTTTTAAATTTATAATATTTATATTAATTATAAAATGTTTAATAATAAAATT ??@+=BDDF?FAAEA:D*?D@FE@?909DBB*??A:D*?D@FE@?909DBB*??>> Writing bisulfite mapping results to 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz Processed 1000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1105:20284:71435_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1105:20284:71435_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1105:20284:71435_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1105:20284:71435_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:7863:45399_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:7863:45399_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:7863:45399_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:7863:45399_1:N:0:TTAGGC' because it was < 2 characters long Processed 2000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1110:20812:68720_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1110:20812:68720_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1110:20812:68720_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1110:20812:68720_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1111:5227:24037_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1111:5227:24037_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1111:5227:24037_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1111:5227:24037_1:N:0:TTAGGC' because it was < 2 characters long Processed 3000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1201:9020:28482_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1201:9020:28482_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1201:9020:28482_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1201:9020:28482_1:N:0:TTAGGC' because it was < 2 characters long Processed 4000000 sequences so far Processed 5000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1765:7763_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1765:7763_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1765:7763_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1765:7763_1:N:0:TTAGGC' because it was < 2 characters long Processed 6000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1216:3752:29619_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1216:3752:29619_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1216:3752:29619_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1216:3752:29619_1:N:0:TTAGGC' because it was < 2 characters long Processed 7000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1301:9827:92122_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1301:9827:92122_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1301:9827:92122_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1301:9827:92122_1:N:0:TTAGGC' because it was < 2 characters long Processed 8000000 sequences so far Processed 9000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:11458:97070_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:11458:97070_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:11458:97070_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:11458:97070_1:N:0:TTAGGC' because it was < 2 characters long Processed 10000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2104:18319:21436_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2104:18319:21436_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2104:18319:21436_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2104:18319:21436_1:N:0:TTAGGC' because it was < 2 characters long Processed 11000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4988:67942_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4988:67942_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4988:67942_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4988:67942_1:N:0:TTAGGC' because it was < 2 characters long Processed 12000000 sequences so far Processed 13000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:1887:7429_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:1887:7429_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:1887:7429_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:1887:7429_1:N:0:TTAGGC' because it was < 2 characters long Processed 14000000 sequences so far Processed 15000000 sequences so far Processed 16000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2210:3775:42371_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2210:3775:42371_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2210:3775:42371_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2210:3775:42371_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:1349:17177_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:1349:17177_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:1349:17177_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:1349:17177_1:N:0:TTAGGC' because it was < 2 characters long Processed 17000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2301:21274:80179_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2301:21274:80179_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2301:21274:80179_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2301:21274:80179_1:N:0:TTAGGC' because it was < 2 characters long Processed 18000000 sequences so far Processed 19000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:2051:79531_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:2051:79531_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:2051:79531_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:2051:79531_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19602:28141_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19602:28141_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19602:28141_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19602:28141_1:N:0:TTAGGC' because it was < 2 characters long Processed 20000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:15573:93548_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:15573:93548_1:N:0:TTAGGC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:15573:93548_1:N:0:TTAGGC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:15573:93548_1:N:0:TTAGGC' because it was < 2 characters long Chromosomal sequence could not be extracted for HWI-ST0747:461:C64YUACXX:1:2313:10645:74727_1:N:0:TTAGGC NC_035789.1 1 Processed 21000000 sequences so far 21462840 reads; of these: 21462840 (100.00%) were unpaired; of these: 18665487 (86.97%) aligned 0 times21462840 reads; of these: 1128346 (214628405.26 (%) aligned exactly 1 time 1669007 (7.78%100.00) aligned >1 times% ) were unpaired; of these:13.03 % overall alignment rate18663973 (86.96%) aligned 0 times 1143220 (5.33%) aligned exactly 1 time 1655647 (7.71%) aligned >1 times 13.04% overall alignment rate Processed 21462840 sequences in total Successfully deleted the temporary file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 21462840 Number of alignments with a unique best hit from the different alignments: 2514461 Mapping efficiency: 11.7% Sequences with no alignments under any condition: 17492919 Sequences did not map uniquely: 1455460 Sequences which were discarded because genomic sequence could not be extracted: 1 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 1262331 ((converted) top strand) CT/GA: 1252129 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 52094029 Total methylated C's in CpG context: 7150599 Total methylated C's in CHG context: 7107885 Total methylated C's in CHH context: 27083754 Total methylated C's in Unknown context: 144425 Total unmethylated C's in CpG context: 1164370 Total unmethylated C's in CHG context: 3157515 Total unmethylated C's in CHH context: 6429906 Total unmethylated C's in Unknown context: 86805 C methylated in CpG context: 86.0% C methylated in CHG context: 69.2% C methylated in CHH context: 80.8% C methylated in Unknown context (CN or CHN): 62.5% Bismark completed in 0d 0h 48m 44s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1002'): /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/sr320/analyses/1002 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz to 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz (28381961 sequences in total) Input file is 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/Cvirg-genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-ST0747:461:C64YUACXX:1:1101:1222:2147_1:N:0:ATCACG 4 * 0 0 * * 0 0 TTATATAAATATTAAATTAATTTTTTTTATAAATTTATATATTATTGAATATTATTATTTAAATAATAAAATTATTGATTTTTTTATGTTTTTAAAATTTT @@FHII>GIE06B?FD=BG:BHGC7=@GA>7@>7AHHC3?235<@?BCBB=BBBBBFHII>GIE06B?FD=BG:BHGC7=@GA>7@>7AHHC3?235<@?BCBB=BBBBB>> Writing bisulfite mapping results to 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1101:19134:34984_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1101:19134:34984_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1101:19134:34984_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1101:19134:34984_1:N:0:ATCACG' because it was < 2 characters long Processed 1000000 sequences so far Processed 2000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:3110:63301_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:3110:63301_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:3110:63301_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:3110:63301_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:2454:84014_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:2454:84014_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:2454:84014_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:2454:84014_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:12245:88213_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:12245:88213_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:12245:88213_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1109:12245:88213_1:N:0:ATCACG' because it was < 2 characters long Processed 3000000 sequences so far Processed 4000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1114:10924:89327_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1114:10924:89327_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1114:10924:89327_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1114:10924:89327_1:N:0:ATCACG' because it was < 2 characters long Processed 5000000 sequences so far Processed 6000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1206:4678:56948_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1206:4678:56948_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1206:4678:56948_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1206:4678:56948_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1647:26486_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1647:26486_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1647:26486_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1647:26486_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4638:39151_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4638:39151_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4638:39151_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4638:39151_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1112:54523_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1112:54523_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1112:54523_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:1112:54523_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4231:58602_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4231:58602_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4231:58602_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:4231:58602_1:N:0:ATCACG' because it was < 2 characters long Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1302:5938:29900_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1302:5938:29900_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1302:5938:29900_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1302:5938:29900_1:N:0:ATCACG' because it was < 2 characters long Processed 10000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21122:92632_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21122:92632_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21122:92632_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21122:92632_1:N:0:ATCACG' because it was < 2 characters long Processed 11000000 sequences so far Processed 12000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1312:13112:3670_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1312:13112:3670_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1312:13112:3670_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1312:13112:3670_1:N:0:ATCACG' because it was < 2 characters long Processed 13000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:3219:98750_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:3219:98750_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:3219:98750_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:3219:98750_1:N:0:ATCACG' because it was < 2 characters long Processed 14000000 sequences so far Processed 15000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:14940:68781_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:14940:68781_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:14940:68781_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:14940:68781_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11600:95027_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11600:95027_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11600:95027_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11600:95027_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:20964:11379_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:20964:11379_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:20964:11379_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:20964:11379_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:9974:15610_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:9974:15610_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:9974:15610_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:9974:15610_1:N:0:ATCACG' because it was < 2 characters long Processed 16000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:17457:19910_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:17457:19910_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:17457:19910_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:17457:19910_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:5607:85747_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:5607:85747_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:5607:85747_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:5607:85747_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:1312:3731_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:1312:3731_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:1312:3731_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:1312:3731_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:14784:10097_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:14784:10097_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:14784:10097_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2111:14784:10097_1:N:0:ATCACG' because it was < 2 characters long Processed 17000000 sequences so far Processed 18000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:4214:96197_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:4214:96197_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:4214:96197_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:4214:96197_1:N:0:ATCACG' because it was < 2 characters long Processed 19000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2203:2670:87092_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2203:2670:87092_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2203:2670:87092_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2203:2670:87092_1:N:0:ATCACG' because it was < 2 characters long Processed 20000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2207:4181:51445_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2207:4181:51445_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2207:4181:51445_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2207:4181:51445_1:N:0:ATCACG' because it was < 2 characters long Processed 21000000 sequences so far Processed 22000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:13300:71607_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:13300:71607_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:13300:71607_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:13300:71607_1:N:0:ATCACG' because it was < 2 characters long Processed 23000000 sequences so far Processed 24000000 sequences so far Processed 25000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:10949:30966_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:10949:30966_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:10949:30966_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2308:10949:30966_1:N:0:ATCACG' because it was < 2 characters long Processed 26000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:17902:83807_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:17902:83807_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:17902:83807_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:17902:83807_1:N:0:ATCACG' because it was < 2 characters long Processed 27000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2314:18540:71196_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2314:18540:71196_1:N:0:ATCACG' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2314:18540:71196_1:N:0:ATCACG' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2314:18540:71196_1:N:0:ATCACG' because it was < 2 characters long Processed 28000000 sequences so far 28381961 reads; of these: 28381961 (100.00%) were unpaired; of these: 23155274 (81.58%) aligned 0 times 2286937 (8.06%) aligned exactly 1 time 2939750 (10.36%) aligned >1 times 18.42% overall alignment rate 28381961 reads; of these: 28381961 (100.00%) were unpaired; of these: 23161959 (81.61%) aligned 0 times 2273722 (8.01%) aligned exactly 1 time 2946280 (10.38%) aligned >1 times 18.39% overall alignment rate Processed 28381961 sequences in total Successfully deleted the temporary file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 28381961 Number of alignments with a unique best hit from the different alignments: 5065524 Mapping efficiency: 17.8% Sequences with no alignments under any condition: 20851008 Sequences did not map uniquely: 2465429 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2539397 ((converted) top strand) CT/GA: 2526127 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 97961269 Total methylated C's in CpG context: 11788210 Total methylated C's in CHG context: 15007666 Total methylated C's in CHH context: 54473521 Total methylated C's in Unknown context: 267880 Total unmethylated C's in CpG context: 1919128 Total unmethylated C's in CHG context: 4473213 Total unmethylated C's in CHH context: 10299531 Total unmethylated C's in Unknown context: 164315 C methylated in CpG context: 86.0% C methylated in CHG context: 77.0% C methylated in CHH context: 84.1% C methylated in Unknown context (CN or CHN): 62.0% Bismark completed in 0d 1h 25m 30s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1002'): /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/sr320/analyses/1002 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz to 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz (31266957 sequences in total) Input file is 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/Cvirg-genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-ST0747:461:C64YUACXX:1:1101:1170:2189_1:N:0:CAGATC 4 * 0 0 * * 0 0 TTTTGTAAATTATAAAAAAATTTATTTTTTATGTAAAAAAATTAAAAAAATAAATAAAAATTGTGAATTTTTAAAAAAATTTATTATATTATTTTTTTTTT @?@DDDDFG>FDHIGIGHHGGEHGGII@GHIIHIGGGEIGGIIHHIHGFC>CCDDDBB?BBCBDD;@BBD:A9A828>BBCDDDDEEDCCD@CDCCCCCCC YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sr320/data/Cvirg-genome/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-ST0747:461:C64YUACXX:1:1101:1170:2189_1:N:0:CAGATC 4 * 0 0 * * 0 0 TTTTGTAAATTATAAAAAAATTTATTTTTTATGTAAAAAAATTAAAAAAATAAATAAAAATTGTGAATTTTTAAAAAAATTTATTATATTATTTTTTTTTT @?@DDDDFG>FDHIGIGHHGGEHGGII@GHIIHIGGGEIGGIIHHIHGFC>CCDDDBB?BBCBDD;@BBD:A9A828>BBCDDDDEEDCCD@CDCCCCCCC YT:Z:UU >>> Writing bisulfite mapping results to 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz Processed 1000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:20622:48261_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:20622:48261_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:20622:48261_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:20622:48261_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:17731:56324_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:17731:56324_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:17731:56324_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:17731:56324_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:16151:59140_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:16151:59140_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:16151:59140_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1104:16151:59140_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:15230:93418_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:15230:93418_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:15230:93418_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:15230:93418_1:N:0:CAGATC' because it was < 2 characters long Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:12184:8723_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:12184:8723_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:12184:8723_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:12184:8723_1:N:0:CAGATC' because it was < 2 characters long Processed 8000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1213:1337:8589_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1213:1337:8589_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1213:1337:8589_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1213:1337:8589_1:N:0:CAGATC' because it was < 2 characters long Processed 9000000 sequences so far Processed 10000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:1593:23757_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:1593:23757_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:1593:23757_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:1593:23757_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:20816:63335_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:20816:63335_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:20816:63335_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1303:20816:63335_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:1662:12898_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:1662:12898_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:1662:12898_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:1662:12898_1:N:0:CAGATC' because it was < 2 characters long Processed 11000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:19760:52595_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:19760:52595_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:19760:52595_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:19760:52595_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21268:81701_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21268:81701_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21268:81701_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:21268:81701_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:20863:96510_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:20863:96510_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:20863:96510_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1304:20863:96510_1:N:0:CAGATC' because it was < 2 characters long Processed 12000000 sequences so far Processed 13000000 sequences so far Processed 14000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:18889:96886_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:18889:96886_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:18889:96886_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:18889:96886_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:20319:83539_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:20319:83539_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:20319:83539_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:20319:83539_1:N:0:CAGATC' because it was < 2 characters long Processed 15000000 sequences so far Processed 16000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11021:73353_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11021:73353_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11021:73353_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:11021:73353_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:19943:85936_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:19943:85936_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:19943:85936_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2106:19943:85936_1:N:0:CAGATC' because it was < 2 characters long Processed 17000000 sequences so far Processed 18000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:14426:25880_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:14426:25880_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:14426:25880_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:14426:25880_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7278:62027_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7278:62027_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7278:62027_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7278:62027_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:8441:63937_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:8441:63937_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:8441:63937_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:8441:63937_1:N:0:CAGATC' because it was < 2 characters long Processed 19000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:8818:17284_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:8818:17284_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:8818:17284_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:8818:17284_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:18046:37999_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:18046:37999_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:18046:37999_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2114:18046:37999_1:N:0:CAGATC' because it was < 2 characters long Processed 20000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2202:1967:66346_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2202:1967:66346_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2202:1967:66346_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2202:1967:66346_1:N:0:CAGATC' because it was < 2 characters long Processed 21000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2205:6485:78695_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2205:6485:78695_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2205:6485:78695_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2205:6485:78695_1:N:0:CAGATC' because it was < 2 characters long Processed 22000000 sequences so far Processed 23000000 sequences so far Processed 24000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:19735:9843_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:19735:9843_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:19735:9843_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:19735:9843_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:4782:52687_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:4782:52687_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:4782:52687_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2213:4782:52687_1:N:0:CAGATC' because it was < 2 characters long Processed 25000000 sequences so far Processed 26000000 sequences so far Processed 27000000 sequences so far Processed 28000000 sequences so far Processed 29000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:17178:97384_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:17178:97384_1:N:0:CAGATC' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:17178:97384_1:N:0:CAGATC' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2311:17178:97384_1:N:0:CAGATC' because it was < 2 characters long Processed 30000000 sequences so far Processed 31000000 sequences so far 31266957 reads; of these: 31266957 (100.00%) were unpaired; of these: 25973782 (83.07%) aligned 0 times 2110208 (6.75%) aligned exactly 1 time 3182967 (10.18%) aligned >1 times 16.93% overall alignment rate 31266957 reads; of these: 31266957 (100.00%) were unpaired; of these: 25960963 (83.03%) aligned 0 times 2117635 (6.77%) aligned exactly 1 time 3188359 (10.20%) aligned >1 times 16.97% overall alignment rate Processed 31266957 sequences in total Successfully deleted the temporary file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 31266957 Number of alignments with a unique best hit from the different alignments: 4744536 Mapping efficiency: 15.2% Sequences with no alignments under any condition: 23775958 Sequences did not map uniquely: 2746463 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 2383630 ((converted) top strand) CT/GA: 2360906 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 98368212 Total methylated C's in CpG context: 13851042 Total methylated C's in CHG context: 15940213 Total methylated C's in CHH context: 56779026 Total methylated C's in Unknown context: 264963 Total unmethylated C's in CpG context: 1480605 Total unmethylated C's in CHG context: 3375451 Total unmethylated C's in CHH context: 6941875 Total unmethylated C's in Unknown context: 127002 C methylated in CpG context: 90.3% C methylated in CHG context: 82.5% C methylated in CHH context: 89.1% C methylated in Unknown context (CN or CHN): 67.6% Bismark completed in 0d 1h 24m 3s ==================== Bismark run complete ==================== Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.1.0/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/Cvirg-genome/ (absolute path is '/gscratch/srlab/sr320/data/Cvirg-genome/)' 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 28 threads. Please monitor performance closely and tune down if needed! Input files to be analysed (in current folder '/gscratch/srlab/sr320/analyses/1002'): /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/srlab/sr320/analyses/1002 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/ chr NC_035780.1 (65668440 bp) chr NC_035781.1 (61752955 bp) chr NC_035782.1 (77061148 bp) chr NC_035783.1 (59691872 bp) chr NC_035784.1 (98698416 bp) chr NC_035785.1 (51258098 bp) chr NC_035786.1 (57830854 bp) chr NC_035787.1 (75944018 bp) chr NC_035788.1 (104168038 bp) chr NC_035789.1 (32650045 bp) chr NC_007175.2 (17244 bp) Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Writing a C -> T converted version of the input file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz to 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz (20811265 sequences in total) Input file is 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sr320/data/Cvirg-genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-ST0747:461:C64YUACXX:1:1101:1199:2076_1:N:0:GCCAAT 4 * 0 0 * * 0 0 GTNTATTTTTAGAGTGGTTTTTTTGGTATGATTTTTTTGTATTATTATGATATTGTTGTATATTTAGGTTGGAGGAGGTATTTTGGAAAAGAATAGATTGG CC#4ADDFHHGHHHIFHHIJJJJJJJHGJJJJJJJIJJJJJJIIHIIJJIJGIJIJJIIIIFIJJIIJ=DGF?CHEBFCDBEDDDD;>> Writing bisulfite mapping results to 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam <<< Reading in the sequence file /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz Processed 1000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:12871:59187_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:12871:59187_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:12871:59187_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1106:12871:59187_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1108:2348:86910_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1108:2348:86910_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1108:2348:86910_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1108:2348:86910_1:N:0:GCCAAT' because it was < 2 characters long Processed 2000000 sequences so far Processed 3000000 sequences so far Processed 4000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:21248:32838_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:21248:32838_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:21248:32838_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:21248:32838_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:3158:72782_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:3158:72782_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:3158:72782_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1208:3158:72782_1:N:0:GCCAAT' because it was < 2 characters long Processed 5000000 sequences so far Processed 6000000 sequences so far Processed 7000000 sequences so far Processed 8000000 sequences so far Processed 9000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:1511:69890_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:1511:69890_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:1511:69890_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1313:1511:69890_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:7707:9858_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:7707:9858_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:7707:9858_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:1314:7707:9858_1:N:0:GCCAAT' because it was < 2 characters long Processed 10000000 sequences so far Processed 11000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4372:80646_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4372:80646_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4372:80646_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2105:4372:80646_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:8451:5720_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:8451:5720_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:8451:5720_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:8451:5720_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5884:32032_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5884:32032_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5884:32032_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5884:32032_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5871:51074_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5871:51074_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5871:51074_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2107:5871:51074_1:N:0:GCCAAT' because it was < 2 characters long Processed 12000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7970:58161_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7970:58161_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7970:58161_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2110:7970:58161_1:N:0:GCCAAT' because it was < 2 characters long Processed 13000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:2639:41096_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:2639:41096_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:2639:41096_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2115:2639:41096_1:N:0:GCCAAT' because it was < 2 characters long Processed 14000000 sequences so far Processed 15000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2209:20955:91417_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2209:20955:91417_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2209:20955:91417_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2209:20955:91417_1:N:0:GCCAAT' because it was < 2 characters long Processed 16000000 sequences so far Processed 17000000 sequences so far Processed 18000000 sequences so far Processed 19000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:18359:28225_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:18359:28225_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:18359:28225_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:18359:28225_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:2236:66609_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:2236:66609_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:2236:66609_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2309:2236:66609_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19176:11466_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19176:11466_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19176:11466_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:19176:11466_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:5317:26651_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:5317:26651_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:5317:26651_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:5317:26651_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:18132:53633_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:18132:53633_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:18132:53633_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2310:18132:53633_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2312:1613:47737_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2312:1613:47737_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2312:1613:47737_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2312:1613:47737_1:N:0:GCCAAT' because it was < 2 characters long Processed 20000000 sequences so far Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2313:11813:83788_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2313:11813:83788_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2313:11813:83788_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2313:11813:83788_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2316:20302:14755_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2316:20302:14755_1:N:0:GCCAAT' because it was < 2 characters long Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2316:20302:14755_1:N:0:GCCAAT' because length (1) <= # seed mismatches (0) Warning: skipping read 'HWI-ST0747:461:C64YUACXX:1:2316:20302:14755_1:N:0:GCCAAT' because it was < 2 characters long 20811265 reads; of these: 20811265 (100.00%) were unpaired; of these: 18944797 (91.03%) aligned 0 times 724662 (3.48%) aligned exactly 1 time 1141806 (5.49%) aligned >1 times 8.97% overall alignment rate 20811265 reads; of these: 20811265 (100.00%) were unpaired; of these: 18955586 (91.08%) aligned 0 times 731036 (3.51%) aligned exactly 1 time 1124643 (5.40%) aligned >1 times 8.92% overall alignment rate Processed 20811265 sequences in total Successfully deleted the temporary file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 20811265 Number of alignments with a unique best hit from the different alignments: 1614710 Mapping efficiency: 7.8% Sequences with no alignments under any condition: 18190123 Sequences did not map uniquely: 1006432 Sequences which were discarded because genomic sequence could not be extracted: 0 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 807395 ((converted) top strand) CT/GA: 807315 ((converted) bottom strand) GA/CT: 0 (complementary to (converted) top strand) GA/GA: 0 (complementary to (converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 31055287 Total methylated C's in CpG context: 3687058 Total methylated C's in CHG context: 4528705 Total methylated C's in CHH context: 18535716 Total methylated C's in Unknown context: 89242 Total unmethylated C's in CpG context: 629367 Total unmethylated C's in CHG context: 1030792 Total unmethylated C's in CHH context: 2643649 Total unmethylated C's in Unknown context: 50723 C methylated in CpG context: 85.4% C methylated in CHG context: 81.5% C methylated in CHH context: 87.5% C methylated in Unknown context (CN or CHN): 63.8% Bismark completed in 0d 0h 37m 38s ==================== Bismark run complete ==================== Processing single-end Bismark output file(s) (SAM format): /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.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 >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam<< for signs of file truncation... Output file is: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam: 2514460 Total number duplicated alignments removed: 736852 (29.30%) Duplicated alignments were found at: 407048 different position(s) Total count of deduplicated leftover sequences: 1777608 (70.70% of total) Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz" Output file is: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam: 5065524 Total number duplicated alignments removed: 1012120 (19.98%) Duplicated alignments were found at: 703343 different position(s) Total count of deduplicated leftover sequences: 4053404 (80.02% of total) Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz" Output file is: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam: 4744536 Total number duplicated alignments removed: 1254221 (26.44%) Duplicated alignments were found at: 719650 different position(s) Total count of deduplicated leftover sequences: 3490315 (73.56% of total) Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam<< for signs of file truncation... skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz" Output file is: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam: 1614710 Total number duplicated alignments removed: 216713 (13.42%) Duplicated alignments were found at: 145753 different position(s) Total count of deduplicated leftover sequences: 1397997 (86.58% of total) skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_035780.1 LN:65668440 skipping header line: @SQ SN:NC_035781.1 LN:61752955 skipping header line: @SQ SN:NC_035782.1 LN:77061148 skipping header line: @SQ SN:NC_035783.1 LN:59691872 skipping header line: @SQ SN:NC_035784.1 LN:98698416 skipping header line: @SQ SN:NC_035785.1 LN:51258098 skipping header line: @SQ SN:NC_035786.1 LN:57830854 skipping header line: @SQ SN:NC_035787.1 LN:75944018 skipping header line: @SQ SN:NC_035788.1 LN:104168038 skipping header line: @SQ SN:NC_035789.1 LN:32650045 skipping header line: @SQ SN:NC_007175.2 LN:17244 skipping header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz" *** Bismark methylation extractor version v0.19.0 *** Trying to determine the type of mapping from the SAM header line of file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Treating file(s) as single-end data (as extracted from @PG line) Summarising Bismark methylation extractor parameters: =============================================================== Bismark single-end SAM format specified (default) Number of cores to be used: 14 Output will be written to the current directory ('/gscratch/srlab/sr320/analyses/1002') 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: '2G'. Temporary directory used for sorting is the output directory Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.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: 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 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.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.1 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.2 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.3 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.4 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.5 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.6 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.7 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.8 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.9 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.10 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.11 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.12 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.13 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 1777608 lines in total Total number of methylation call strings processed: 1777608 Final Cytosine Methylation Report ================================= Total number of C's analysed: 35349838 Total methylated C's in CpG context: 4749120 Total methylated C's in CHG context: 5059491 Total methylated C's in CHH context: 18152955 Total C to T conversions in CpG context: 832012 Total C to T conversions in CHG context: 2078433 Total C to T conversions in CHH context: 4477827 C methylated in CpG context: 85.1% C methylated in CHG context: 70.9% C methylated in CHH context: 80.2% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.1.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.2.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.3.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.4.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.5.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.6.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.7.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.8.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.9.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.10.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.11.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.12.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.13.mbias 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 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_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CHG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CHH_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt was empty -> deleted CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1002/CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt /gscratch/srlab/sr320/analyses/1002/CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt Writing bedGraph to file: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.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 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt to merged temp file Sorting input file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.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_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.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: 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: 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: 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: 4000000 Processed lines: 4000000 Processed lines: 4000000 Now waiting for all child processes to complete Finished processing child process. Exiting.. Processed lines: 4000000 Finished processing child process. Exiting.. 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 Finished processing child process. Exiting.. Processed lines: 4000000 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: '20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.1 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.2 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.3 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.4 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.5 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.6 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.7 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.8 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.9 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.10 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.11 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.12 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.13 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 4053404 lines in total Total number of methylation call strings processed: 4053404 Final Cytosine Methylation Report ================================= Total number of C's analysed: 76917247 Total methylated C's in CpG context: 9175210 Total methylated C's in CHG context: 12020501 Total methylated C's in CHH context: 43014122 Total C to T conversions in CpG context: 1511866 Total C to T conversions in CHG context: 3290919 Total C to T conversions in CHH context: 7904629 C methylated in CpG context: 85.9% C methylated in CHG context: 78.5% C methylated in CHH context: 84.5% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.1.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.2.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.3.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.4.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.5.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.6.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.7.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.8.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.9.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.10.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.11.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.12.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.13.mbias 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 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_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CHG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CHH_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt was empty -> deleted CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1002/CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt /gscratch/srlab/sr320/analyses/1002/CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt Writing bedGraph to file: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.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 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt to merged temp file Sorting input file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.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_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.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: 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: 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: 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 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.. 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: '20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.1 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.2 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.3 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.4 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.5 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.6 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.7 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.8 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.9 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.10 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.11 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.12 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.13 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 3490315 lines in total Total number of methylation call strings processed: 3490315 Final Cytosine Methylation Report ================================= Total number of C's analysed: 69554871 Total methylated C's in CpG context: 9597849 Total methylated C's in CHG context: 11742690 Total methylated C's in CHH context: 40005921 Total C to T conversions in CpG context: 1067280 Total C to T conversions in CHG context: 2239960 Total C to T conversions in CHH context: 4901171 C methylated in CpG context: 90.0% C methylated in CHG context: 84.0% C methylated in CHH context: 89.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.1.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.2.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.3.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.4.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.5.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.6.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.7.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.8.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.9.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.10.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.11.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.12.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.13.mbias 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 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_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CHG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CHH_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt was empty -> deleted CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1002/CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt /gscratch/srlab/sr320/analyses/1002/CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt Writing bedGraph to file: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.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 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt to merged temp file Sorting input file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>/gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam<< for signs of file truncation... Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam Now reading in Bismark result file /gscratch/srlab/sr320/analyses/1002/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.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_035780.1 LN:65668440 skipping SAM header line: @SQ SN:NC_035781.1 LN:61752955 skipping SAM header line: @SQ SN:NC_035782.1 LN:77061148 skipping SAM header line: @SQ SN:NC_035783.1 LN:59691872 skipping SAM header line: @SQ SN:NC_035784.1 LN:98698416 skipping SAM header line: @SQ SN:NC_035785.1 LN:51258098 skipping SAM header line: @SQ SN:NC_035786.1 LN:57830854 skipping SAM header line: @SQ SN:NC_035787.1 LN:75944018 skipping SAM header line: @SQ SN:NC_035788.1 LN:104168038 skipping SAM header line: @SQ SN:NC_035789.1 LN:32650045 skipping SAM header line: @SQ SN:NC_007175.2 LN:17244 skipping SAM header line: @PG ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.1.0 --score_min L,0,-0.6 -genome /gscratch/srlab/sr320/data/Cvirg-genome -p 28 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.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: 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 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.. 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: '20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt' Merging from these individual files: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.1 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.2 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.3 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.4 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.5 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.6 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.7 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.8 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.9 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.10 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.11 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.12 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.13 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.14 Processed 1397997 lines in total Total number of methylation call strings processed: 1397997 Final Cytosine Methylation Report ================================= Total number of C's analysed: 26386132 Total methylated C's in CpG context: 3157239 Total methylated C's in CHG context: 3948194 Total methylated C's in CHH context: 15546039 Total C to T conversions in CpG context: 537605 Total C to T conversions in CHG context: 887398 Total C to T conversions in CHH context: 2309657 C methylated in CpG context: 85.4% C methylated in CHG context: 81.6% C methylated in CHH context: 87.1% Merging individual M-bias reports into overall M-bias statistics from these 14 individual files: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.1.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.2.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.3.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.4.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.5.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.6.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.7.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.8.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.9.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.10.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.11.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.12.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.13.mbias 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.14.mbias Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read length for M-Bias plot Maximum read length of Read 1: 101 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_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept CHG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CHG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept CHH_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CHH_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt was empty -> deleted CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data -> kept Using these input files: CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.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: 2G Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/srlab/sr320/analyses/1002/CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt /gscratch/srlab/sr320/analyses/1002/CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt Writing bedGraph to file: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.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 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt to merged temp file Sorting input file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G) Successfully deleted the temporary input file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ...