Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/srlab/programs/samtools-1.20/samtools' Reference genome folder provided is /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ (absolute path is '/mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/)' FastQ format assumed (by default) Attention: early reports suggested that high values of -p to have diminishing returns. Please test different values using a small subset of data for your hardware setting. Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark'): /mmfs1/gscratch/coenv/sr320/cod-bs/74B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/74B_2.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!) Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/output/16-bismark Now reading in and storing sequence information of the genome specified in: /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /mmfs1/gscratch/coenv/sr320/cod-bs/74B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/74B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 74B_1.fastq.gz to 74B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 74B_1.fastq.gz (51345451 sequences in total) Writing a G -> A converted version of the input file 74B_2.fastq.gz to 74B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 74B_2.fastq.gz (51345451 sequences in total) Input files are 74B_1.fastq.gz_C_to_T.fastq and 74B_2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ with the specified options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 74B_1.fastq.gz_C_to_T.fastq and 74B_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00160:538:22WG5VLT4:6:1101:23165:1042_1:N:0:CGTTGCAA+ATNGAGCG/1 77 * 0 0 * * 0 0 TNGAGTTTTGTTTGAGGTGAGGTATGTTTTTTGTGTTGAATTATGTGTTGGTTTGGTTATTTTGTGGTTATTTTGGTGTTAAATGTTAGTTGGGTGGTGGGTTGGTGGATATGGATGGGGTTATTGTGTTGATTATATTTGTGATGAGTTG I#IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00160:538:22WG5VLT4:6:1101:23165:1042_2:N:0:CGTTGCAA+ATNGAGCG/2 141 * 0 0 * * 0 0 AAAAAAATACTAACAACAACTCATCAACATCCAATCACAAATCTTCCAACTCATCACAAATATAATCAACACAATAACCCCATCCATATCCACCAACCCACCACCCAACTAACATTTAACACCAAAATAACCACAAAATAACCAAACCAAC IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 74B_1.fastq.gz_C_to_T.fastq and 74B_2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.8 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00160:538:22WG5VLT4:6:1101:23165:1042_1:N:0:CGTTGCAA+ATNGAGCG/1 83 NC_082389.1_GA_converted 13498235 42 151M = 13498191 -195 CAACTCATCACAAATATAATCAACACAATAACCCCATCCATATCCACCAACCCACCACCCAACTAACATTTAACACCAAAATAACCACAAAATAACCAAACCAACACATAATTCAACACAAAAAACATACCTCACCTCAAACAAAACTCNA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII#I AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:43T105C1 YS:i:-35 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:23165:1042_2:N:0:CGTTGCAA+ATNGAGCG/2 163 NC_082389.1_GA_converted 13498191 42 4M2I145M = 13498235 195 AAAAAAATACTAACAACAACTCATCAACATCCAATCACAAATCTTCCAACTCATCACAAATATAATCAACACAATAACCCCATCCATATCCACCAACCCACCACCCAACTAACATTTAACACCAAAATAACCACAAAATAACCAAACCAAC IIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-35 XN:i:0 XM:i:4 XO:i:1 XG:i:2 NM:i:6 MD:Z:1C1C0C82T61 YS:i:-7 YT:Z:CP >>> Writing bisulfite mapping results to 74B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/74B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/74B_2.fastq.gz Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1111:33668:8662_1:N:0:CGTTGCAA+ATAGAGCG NC_082396.1 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1163:32131:8606_1:N:0:CGTTGCAA+ATAGAGCG NC_082394.1 22312308 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1203:39301:16282_1:N:0:CGTTGCAA+ATAGAGCG NC_082387.1 3 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1219:4229:13145_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077811 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1219:28020:20177_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077815 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1221:24969:27195_1:N:0:CGTTGCAA+ATAGAGCG NC_082388.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1229:32317:16296_1:N:0:CGTTGCAA+ATAGAGCG NC_082388.1 28186528 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1240:40393:27475_1:N:0:CGTTGCAA+ATAGAGCG NC_082387.1 3 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1265:34105:5244_1:N:0:CGTTGCAA+ATAGAGCG NC_082383.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1265:34122:5244_1:N:0:CGTTGCAA+ATAGAGCG NC_082383.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1267:46373:27489_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077829 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1267:46365:27503_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077829 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1267:46381:27503_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077829 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1313:1890:28567_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077814 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1318:13519:26396_1:N:0:CGTTGCAA+ATAGAGCG NC_082386.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1321:50533:20485_1:N:0:CGTTGCAA+ATAGAGCG NC_036931.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1323:21441:25318_1:N:0:CGTTGCAA+ATAGAGCG NC_082402.1 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1364:29048:14335_1:N:0:CGTTGCAA+ATAGAGCG NC_082382.1 26289613 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1367:20818:16339_1:N:0:CGTTGCAA+ATAGAGCG NC_082383.1 23805011 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1409:10436:6295_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077812 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1423:41210:23791_1:N:0:CGTTGCAA+ATAGAGCG NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1426:48744:6575_1:N:0:CGTTGCAA+ATAGAGCG NC_082396.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1429:48218:3339_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1429:48210:3353_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077815 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1430:28336:29100_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077808 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1449:24055:24575_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077818 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1497:32851:28175_1:N:0:CGTTGCAA+ATAGAGCG NC_082385.1 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2115:19240:23609_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077806 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2115:19256:23609_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077806 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2119:20786:29506_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077820 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2141:23108:8256_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2148:1963:14153_1:N:0:CGTTGCAA+ATAGAGCG NC_082393.1 27586976 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2174:11350:19364_1:N:0:CGTTGCAA+ATAGAGCG NC_082393.1 2 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2229:26652:1840_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077817 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2250:39875:15092_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077818 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2259:32285:23272_1:N:0:CGTTGCAA+ATAGAGCG NC_082385.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2264:23100:8914_1:N:0:CGTTGCAA+ATAGAGCG NC_082398.1 16295406 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2285:17468:28385_1:N:0:CGTTGCAA+ATAGAGCG NC_082400.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2293:46721:17529_1:N:0:CGTTGCAA+ATAGAGCG NC_082382.1 26289619 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2331:21044:26452_1:N:0:CGTTGCAA+ATAGAGCG NC_082387.1 2 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2338:26741:7682_1:N:0:CGTTGCAA+ATAGAGCG NC_082388.1 28186550 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2342:47741:6183_1:N:0:CGTTGCAA+ATAGAGCG NC_082399.1 21077819 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2369:22145:8410_1:N:0:CGTTGCAA+ATAGAGCG NC_082396.1 24646065 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2403:19936:5342_1:N:0:CGTTGCAA+ATAGAGCG NC_082393.1 3 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2405:34526:22054_1:N:0:CGTTGCAA+ATAGAGCG NC_082394.1 22312306 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2429:27915:22740_1:N:0:CGTTGCAA+ATAGAGCG NC_082386.1 22175831 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2435:7093:10988_1:N:0:AGTTGCAA+ATAGAGCG NC_082398.1 16295386 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2438:18916:11702_1:N:0:CGTTGCAA+ATAGAGCG NC_082387.1 1 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far