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/71B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/71B_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/71B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/71B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 71B_1.fastq.gz to 71B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 71B_1.fastq.gz (56926757 sequences in total) Writing a G -> A converted version of the input file 71B_2.fastq.gz to 71B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 71B_2.fastq.gz (56926757 sequences in total) Input files are 71B_1.fastq.gz_C_to_T.fastq and 71B_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 71B_1.fastq.gz_C_to_T.fastq and 71B_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: LH00160:538:22WG5VLT4:6:1101:25430:1042_1:N:0:ACGTCATT+CANACGTT/1 77 * 0 0 * * 0 0 ANAGGTAGAATTAGAAGTATAGATTTAAATTTATATTGAAAAAATATATTTTTTTGTAGTTTATTTATTATGTGTATTATATTTGTTATAGTATAGTGTAGTAAAGATATGATATAGTATTAAAGGTTGGGTATGGGATTTGTGAAATGTT I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP LH00160:538:22WG5VLT4:6:1101:25430:1042_2:N:0:ACGTCATT+CANACGTT/2 141 * 0 0 * * 0 0 AAAAATCCAAATACTTAAAATAAATAAAATCAAAATCAACACTAAAAAAAAAAAAAAAAAACCCCTTAAACTCTCCATTTTCAAAACCCCCCCAACTTCCACAAACCCCATCCCCAACCTTTCACCCCTTCTCCCCTCTTTCCCACACCCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIII--III99I-99-I--9-----99999-999--9-99-9---9-999-9-9-----9-9---9--I9--9-99-----9-----9-9-9------- YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 71B_1.fastq.gz_C_to_T.fastq and 71B_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: LH00160:538:22WG5VLT4:6:1101:25430:1042_1:N:0:ACGTCATT+CANACGTT/1 77 * 0 0 * * 0 0 ANAGGTAGAATTAGAAGTATAGATTTAAATTTATATTGAAAAAATATATTTTTTTGTAGTTTATTTATTATGTGTATTATATTTGTTATAGTATAGTGTAGTAAAGATATGATATAGTATTAAAGGTTGGGTATGGGATTTGTGAAATGTT I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIII YT:Z:UP LH00160:538:22WG5VLT4:6:1101:25430:1042_2:N:0:ACGTCATT+CANACGTT/2 141 * 0 0 * * 0 0 AAAAATCCAAATACTTAAAATAAATAAAATCAAAATCAACACTAAAAAAAAAAAAAAAAAACCCCTTAAACTCTCCATTTTCAAAACCCCCCCAACTTCCACAAACCCCATCCCCAACCTTTCACCCCTTCTCCCCTCTTTCCCACACCCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIII9IIIIII--III99I-99-I--9-----99999-999--9-99-9---9-999-9-9-----9-9---9--I9--9-99-----9-----9-9-9------- YT:Z:UP >>> Writing bisulfite mapping results to 71B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/71B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/71B_2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1141:37747:17011_1:N:0:GCGTCATT+CAGACGTT NC_082387.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1144:43314:25191_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077817 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1168:45548:14489_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077812 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1168:45540:14504_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077812 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1184:2780:1784_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077820 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1226:13810:26032_1:N:0:GCGTCATT+CAGACGTT NC_082383.1 23805007 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1246:28894:11576_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077821 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1265:46859:3087_1:N:0:GCGTCATT+CAGACGTT NC_082396.1 24646079 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1270:43290:8676_1:N:0:GCGTCATT+CAGACGTT NC_036931.1 16435 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1282:48153:26256_1:N:0:GCGTCATT+CAGACGTT NC_082391.1 23727853 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1283:36808:14910_1:N:0:GCGTCATT+CAGACGTT NC_082383.1 23805012 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1288:8283:26438_1:N:0:GCGTCATT+CAGACGTT NC_082400.1 17993475 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1350:50711:14377_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077817 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1350:50719:14391_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077817 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1351:42554:4544_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077813 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1440:42772:25346_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077817 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1447:33296:2331_1:N:0:GCGTCATT+CAGACGTT NC_082396.1 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2104:23318:3830_1:N:0:GCGTCATT+CAGACGTT NC_082382.1 26289589 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2240:45426:4278_1:N:0:GCGTCATT+CAGACGTT NC_036931.1 1 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2271:17532:2079_1:N:0:GCGTCATT+CAGACGTT NC_082396.1 2 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2280:12677:18300_1:N:0:GCGTCATT+CAGACGTT NC_082390.1 23393724 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2281:26248:17949_1:N:0:GCGTCATT+CAGACGTT NC_082390.1 23393724 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2284:3784:28287_1:N:0:GCGTCATT+CAGACGTT NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2284:3800:28287_1:N:0:GCGTCATT+CAGACGTT NC_082392.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2287:46770:12767_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077834 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2287:46762:12781_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077834 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2287:46778:12781_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077834 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2312:31815:7360_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077817 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2356:18884:5426_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077809 Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2377:51803:9993_1:N:0:GCGTCATT+CAGACGTT NC_082392.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2383:5718:8270_1:N:0:GCGTCATT+CAGACGTT NC_082399.1 21077820 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2388:45038:4306_1:N:0:GCGTCATT+CAGACGTT NC_082383.1 23805024