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/72B_1.fastq.gz /mmfs1/gscratch/coenv/sr320/cod-bs/72B_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/72B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/72B_2.fastq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 72B_1.fastq.gz to 72B_1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 72B_1.fastq.gz (59130634 sequences in total) Writing a G -> A converted version of the input file 72B_2.fastq.gz to 72B_2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 72B_2.fastq.gz (59130634 sequences in total) Input files are 72B_1.fastq.gz_C_to_T.fastq and 72B_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 72B_1.fastq.gz_C_to_T.fastq and 72B_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: LH00160:538:22WG5VLT4:6:1101:23148:1042_1:N:0:ATCCGGTA+GANCGATA/1 99 NC_082399.1_CT_converted 20153488 27 151M = 20153514 177 TNATGGGTGAAAGTTATTATTAGTGTTGGGGAGTTATTGGTGTTATATATTTAGAATTTAAATTATAGTTAATTGTATTTTGTTATAGTTATAATTTAAATAGTTGGTATTTATAATATAGTTATAATGTTGAAATTAATGGATTATATGA I#IIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-1 XS:i:-107 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:1T149 YS:i:-18 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:23148:1042_2:N:0:ATCCGGTA+GANCGATA/2 147 NC_082399.1_CT_converted 20153514 27 151M = 20153488 -177 TGGGGAGTTATTGGTGTTATATATTTAGAATTTAAATTATAGTTAATTGTATTTTGTTATAGTTATAATTTAAATAGTTGGTATTTATAATATAGTTATAATGTTGAAATTAATGGATTATATGAAGATATTTTTGTTTTAGTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-108 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:143A0G3A2 YS:i:-1 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 72B_1.fastq.gz_C_to_T.fastq and 72B_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: LH00160:538:22WG5VLT4:6:1101:23148:1042_1:N:0:ATCCGGTA+GANCGATA/1 83 NC_082389.1_GA_converted 6019306 2 116M9I4M5I3M3I2M3I6M = 6019280 -157 TCATATAATCCATTAATTTCAACATTATAACTATATTATAAATACCAACTATTTAAATTATAACTATAACAAAATACAATTAACTATAATTTAAATTCTAAATATATAACACCAATAACTCCCCAACACTAATAATAACTTTCACCCATNA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIII#I AS:i:-111 XS:i:-114 XN:i:0 XM:i:6 XO:i:4 XG:i:20 NM:i:26 MD:Z:24A12C4A50T10C24T1 YS:i:-77 YT:Z:CP LH00160:538:22WG5VLT4:6:1101:23148:1042_2:N:0:ATCCGGTA+GANCGATA/2 163 NC_082389.1_GA_converted 6019280 2 143M4I4M = 6019306 157 AAAAAAAAACTAAAACAAAAATATCTTCATATAATCCATTAATTTCAACATTATAACTATATTATAAATACCAACTATTTAAATTATAACTATAACAAAATACAATTAACTATAATTTAAATTCTAAATATATAACACCAATAACTCCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-77 XS:i:-89 XN:i:0 XM:i:10 XO:i:1 XG:i:4 NM:i:14 MD:Z:2T3C0T17A24A12C4A50T10C13A2 YS:i:-111 YT:Z:CP >>> Writing bisulfite mapping results to 72B_pe.bam <<< Reading in the sequence files /mmfs1/gscratch/coenv/sr320/cod-bs/72B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/72B_2.fastq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1134:30642:17907_1:N:0:ATCCGGTA+GACCGATA NC_082382.1 26289619 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1138:48226:1812_1:N:0:ATCCGGTA+GACCGATA NC_082397.1 1 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1160:44844:19995_1:N:0:ATCCGGTA+GACCGATA NC_082387.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1173:17783:3213_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1173:17791:3227_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1209:33539:14069_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077815 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1212:50994:21704_1:N:0:ATCCGGTA+GACCGATA NC_082395.1 3 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1214:24670:25388_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 22175838 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1229:50015:18580_1:N:0:ATCCGGTA+GACCGATA NC_082392.1 2 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1252:8704:20247_1:N:0:ATCCGGTA+GACCGATA NC_036931.1 16431 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1257:41890:25304_1:N:0:ATCCGGTA+GACCGATA NC_082390.1 23393734 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1266:29922:25177_1:N:0:ATCCGGTA+GACCGATA NC_082395.1 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1269:20381:27125_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 1 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1296:11245:5482_1:N:0:ATCCGGTA+GACCGATA NC_082395.1 26048657 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1353:45329:23693_1:N:0:ATCCGGTA+GACCGATA NC_082387.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1359:33887:13747_1:N:0:ATCCGGTA+GACCGATA NC_082387.1 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1367:12920:5216_1:N:0:ATCCGGTA+GACCGATA NC_082391.1 23727853 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1371:49829:22880_1:N:0:ATCCGGTA+GACCGATA NC_036931.1 16422 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 LH00160:538:22WG5VLT4:6:1433:22072:16100_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1439:32705:6015_1:N:0:ATCCGGTA+GACCGATA NC_082387.1 1 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1446:6050:29184_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077817 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1447:26855:12500_1:N:0:ATCCGGTA+GACCGATA NC_082391.1 23727853 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:1459:29145:22488_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077812 Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2116:28732:13901_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077818 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2144:32786:28035_1:N:0:ATCCGGTA+GACCGATA NC_082396.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2149:24565:17613_1:N:0:ATCCGGTA+GACCGATA NC_082382.1 26289605 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2151:23068:7402_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077820 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2165:3484:19644_1:N:0:ATCCGGTA+GACCGATA NC_082386.1 22175829 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2168:40579:15498_1:N:0:ATCCGGTA+GACCGATA NC_082395.1 26048643 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2173:28546:13915_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077812 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2181:17193:4572_1:N:0:ATCCGGTA+GACCGATA NC_082391.1 23727853 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2205:1267:5244_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077813 Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2205:1259:5258_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077813 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2241:13130:8718_1:N:0:ATCCGGTA+GACCGATA NC_082387.1 2 Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2249:26717:12598_1:N:0:ATCCGGTA+GACCGATA NC_082402.1 1 Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2286:29914:14209_1:N:0:ATCCGGTA+GACCGATA NC_082390.1 23393723 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2294:30286:4096_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077808 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2309:27292:16815_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077819 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:538:22WG5VLT4:6:2319:9861:25304_1:N:0:ATCCGGTA+GACCGATA NC_082399.1 21077817 Processed 47000000 sequence pairs so far