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/68B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/68B_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/68B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/68B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 68B_1.fastq.gz to 68B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 68B_1.fastq.gz (49733210 sequences in total) Writing a G -> A converted version of the input file 68B_2.fastq.gz to 68B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 68B_2.fastq.gz (49733210 sequences in total) Input files are 68B_1.fastq.gz_C_to_T.fastq and 68B_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 68B_1.fastq.gz_C_to_T.fastq and 68B_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: LH00160:538:22WG5VLT4:6:1101:21983:1042_1:N:0:GCACAACT+CTNAACGT/1 99 NC_082400.1_CT_converted 12447549 40 151M = 12447574 168 GNGATATAAGTTATTAGTTATGGTATGATATATTATGTTATGGTGATATATTTAAAGAGATTTGGTTAGTTATGAGATATTGTTATTTATGGAGATGTAATGTAGAAGATATGATGAGTTATGGTGATGTAAGAGATAAATTATGGTGATA I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:1A36A112 YS:i:-47 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:21983:1042_2:N:0:GCACAACT+CTNAACGT/2 147 NC_082400.1_CT_converted 12447574 40 138M8I5M = 12447549 -168 TGATATATTATGTTATGGTGATATATTTAAAGAGATTTGGTTAGTTATGAGATATTGTTATTTATGGAGATGTAATGTAGAAGATATGATGAGTTATGGTGATGTAAGAGATAAATTATGGTGATATAATGTTAGAGATTTTTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIII AS:i:-47 XN:i:0 XM:i:3 XO:i:1 XG:i:8 NM:i:11 MD:Z:13A125A1G1 YS:i:-7 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 68B_1.fastq.gz_C_to_T.fastq and 68B_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: LH00160:538:22WG5VLT4:6:1101:21983:1042_1:N:0:GCACAACT+CTNAACGT/1 77 * 0 0 * * 0 0 GNGATATAAGTTATTAGTTATGGTATGATATATTATGTTATGGTGATATATTTAAAGAGATTTGGTTAGTTATGAGATATTGTTATTTATGGAGATGTAATGTAGAAGATATGATGAGTTATGGTGATGTAAGAGATAAATTATGGTGATA I#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00160:538:22WG5VLT4:6:1101:21983:1042_2:N:0:GCACAACT+CTNAACGT/2 141 * 0 0 * * 0 0 AAAAAAAAAAAAATCTCTAACATTATATCACCATAATTTATCTCTTACATCACCATAACTCATCATATCTTCTACATTACATCTCCATAAATAACAATATCTCATAACTAACCAAATCTCTTTAAATATATCACCATAACATAATATATCA IIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 68B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/68B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/68B_2.fastq.gz Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1110:24735:7570_1:N:0:GCACAACT+CTGAACGT NC_082393.1 3 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1113:46810:8578_1:N:0:GCACAACT+CTGAACGT NC_082393.1 2 Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1143:15121:8662_1:N:0:GCACAACT+CTGAACGT NC_082391.1 23727853 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1143:15113:8676_1:N:0:GCACAACT+CTGAACGT NC_082391.1 23727853 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1153:15631:2457_1:N:0:GCACAACT+CTGAACGT NC_082382.1 26289596 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1187:8243:16647_1:N:0:GCACAACT+CTGAACGT NC_082387.1 3 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1189:9416:18482_1:N:0:GCACAACT+CTGAACGT NC_082382.1 26289621 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1216:46446:11450_1:N:0:GCACAACT+CTGAACGT NC_082391.1 23727853 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1217:46276:4152_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077815 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1253:25576:28974_1:N:0:GCACAACT+CTGAACGT NC_082387.1 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1279:33879:11240_1:N:0:GCACAACT+CTGAACGT NC_082395.1 26048644 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1313:42367:21816_1:N:0:GCACAACT+CTGAACGT NC_082396.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1344:30423:5791_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077818 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1352:29072:4124_1:N:0:GCACAACT+CTGAACGT NC_082386.1 1 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1365:18390:18468_1:N:0:GCACAACT+CTGAACGT NC_082386.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1378:18107:2933_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077822 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 LH00160:538:22WG5VLT4:6:1421:35780:25570_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077812 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1432:24548:10105_1:N:0:GCACAACT+CTGAACGT NC_082393.1 1 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 LH00160:538:22WG5VLT4:6:2105:40037:17277_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077819 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2106:21805:5300_1:N:0:GCACAACT+CTGAACGT NC_082389.1 23759922 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2166:33474:5833_1:N:0:GCACAACT+CTGAACGT NC_082392.1 2 Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2193:17071:28399_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077820 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2193:17087:28399_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077820 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2230:35562:20345_1:N:0:GCACAACT+CTGAACGT NC_082396.1 2 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2256:5645:17809_1:N:0:GCACAACT+CTGAACGT NC_082387.1 1 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2290:37366:27727_1:N:0:GCACAACT+CTGAACGT NC_036931.1 16416 Processed 38000000 sequence pairs so far Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2370:1615:14896_1:N:0:ACACAACT+CTGAACGT NC_082386.1 2 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2376:40369:27489_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2376:40385:27489_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077815 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2390:16715:29072_1:N:0:GCACAACT+CTGAACGT NC_082402.1 2 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2414:28206:26102_1:N:0:GCACAACT+CTGAACGT NC_082398.1 16295393 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2415:11941:17249_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077811 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2423:15234:13285_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077819 Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2444:7441:14475_1:N:0:GCACAACT+CTGAACGT NC_082399.1 21077819