Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools' Reference genome folder provided is ../data/ (absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/)' 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 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code'): ../data/78M_R1.fastp-trim.fq.gz ../data/78M_R2.fastp-trim.fq.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: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/01.2-bismark/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../data/78M_R1.fastp-trim.fq.gz and ../data/78M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 78M_R1.fastp-trim.fq.gz to 78M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 78M_R1.fastp-trim.fq.gz (97080726 sequences in total) Writing a G -> A converted version of the input file 78M_R2.fastp-trim.fq.gz to 78M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 78M_R2.fastp-trim.fq.gz (97080726 sequences in total) Input files are 78M_R1.fastp-trim.fq.gz_C_to_T.fastq and 78M_R2.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ with the specified options: -q --score-min L,0,-1.0 -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 78M_R1.fastp-trim.fq.gz_C_to_T.fastq and 78M_R2.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1688:1014_1:N:0:TGTGACTG+AGCATATC/1 77 * 0 0 * * 0 0 TGGGATTTTATTTTAATATATTATAATTAATTTAGTTTTATGTAAGTTAGTGTGGGTTTGAGATAGTTTGTGTTTTTTATAAATTATATTATTTATATTGAAGAGATTAATTTATATTTTATTATGTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1688:1014_2:N:0:TGTGACTG+AGCATATC/2 141 * 0 0 * * 0 0 TAAACATCTTTTAACAAAATAATAAACCTAACTAATTACAATATCAACATTATTTTTCTATCTTAATTCAACAAACACACATTTTACAATCAATAACATTCAAAACAAAACAATTAATAAACCAAAACAAT IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 78M_R1.fastp-trim.fq.gz_C_to_T.fastq and 78M_R2.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:1688:1014_1:N:0:TGTGACTG+AGCATATC/1 77 * 0 0 * * 0 0 TGGGATTTTATTTTAATATATTATAATTAATTTAGTTTTATGTAAGTTAGTGTGGGTTTGAGATAGTTTGTGTTTTTTATAAATTATATTATTTATATTGAAGAGATTAATTTATATTTTATTATGTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1688:1014_2:N:0:TGTGACTG+AGCATATC/2 141 * 0 0 * * 0 0 TAAACATCTTTTAACAAAATAATAAACCTAACTAATTACAATATCAACATTATTTTTCTATCTTAATTCAACAAACACACATTTTACAATCAATAACATTCAAAACAAAACAATTAATAAACCAAAACAAT IIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9I-IIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 78M_pe.bam <<< Reading in the sequence files ../data/78M_R1.fastp-trim.fq.gz and ../data/78M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1118:7166:2289_1:N:0:TGTGACTG+AGCCTATC NW_026963772.1 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1124:7085:4306_1:N:0:CGTGACTG+AGCCTATC NW_026963510.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:33369:19574_1:N:0:TGTGACTG+AGCCTATC NW_026963587.1 1 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1138:22687:21928_1:N:0:TGTGACTG+AGCCTATC NW_026963293.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1139:28951:25233_1:N:0:TGTGACTG+AGCCTATC NW_026963804.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1143:46867:21395_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1147:15032:29268_1:N:0:TGTGACTA+AGCCTATC NW_026963415.1 1 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:51746:26928_1:N:0:TGTGACTG+AGCCTATC NW_026963299.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:51763:26928_1:N:0:TGTGACTG+AGCCTATC NW_026963299.1 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1159:10217:26564_1:N:0:TGTGACTG+AGCCTATC NW_026963372.1 501127 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1160:5006:3255_1:N:0:TGTGACTG+AGCCTATC NW_026963501.1 19455 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1169:24249:21101_1:N:0:TGTGACTG+AGCCTATC NW_026963365.1 61330 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1172:39098:3830_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 2 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1180:16068:11814_1:N:0:TGTGACTG+AGCCTATC NW_026963794.1 13157 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1189:25997:17683_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1191:19839:22964_1:N:0:TGTGACTG+AGCCTATC NW_026963342.1 1 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1204:17565:14798_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1217:30537:15484_1:N:0:TGTGACTG+AGCCTATC NC_086376.1 96324267 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1219:30003:12374_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 3 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1226:31394:23020_1:N:0:TGTGACTG+AGCCTATC NW_026963372.1 501127 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1231:23569:28441_1:N:0:TGTGACTG+AGCCTATC NW_026963706.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1239:31864:21675_1:N:0:TGTGACTG+AGCCTATC NW_026963528.1 20825 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1240:19345:27181_1:N:0:TGTGACTG+AGCCTATC NW_026963644.1 30473 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1253:29379:3059_1:N:0:TGTGACTG+AGCCTATC NW_026963711.1 22990 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1259:38823:14532_1:N:0:TGTGACTG+AGCCTATC NW_026963710.1 22501 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1266:36169:20751_1:N:0:TGTGACTG+AGCCTATC NW_026963369.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1270:35263:22880_1:N:0:TGTGACTG+AGCCTATC NW_026963599.1 40052 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1270:35279:22880_1:N:0:TGTGACTG+AGCCTATC NW_026963599.1 40052 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1270:35271:22894_1:N:0:TGTGACTG+AGCCTATC NW_026963599.1 40052 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1277:5912:8270_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1281:28611:3213_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1305:51924:2835_1:N:0:TGTGACTG+AGCCTATC NW_026963636.1 18742 Processed 27000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:1340:39317:24827_1:N:0:TGTGACTG+AGCCTATC NW_026963308.1 1 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1343:51398:26718_1:N:0:TGTGACTG+AGCCTATC NW_026963533.1 25119 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1353:18366:23917_1:N:0:TGTGACTG+AGCCTATC NW_026963308.1 2 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1361:48938:26830_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1369:33215:25584_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1370:43962:18468_1:N:0:TGTGACTG+AGCCTATC NW_026963303.1 249870 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1383:4973:6701_1:N:0:TGTGACTG+AGCCTATC NW_026963722.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:45022:16100_1:N:0:TGTGACTG+AGCCTATC NW_026963684.1 18480 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:45038:16100_1:N:0:TGTGACTG+AGCCTATC NW_026963684.1 18480 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1387:45054:16100_1:N:0:TGTGACTG+AGCCTATC NW_026963684.1 18480 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1390:12580:15974_1:N:0:TGTGACTG+AGCCTATC NW_026963369.1 120965 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1393:13438:16311_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 1 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1407:25989:9293_1:N:0:TGTGACTG+AGCCTATC NW_026963553.1 40190 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1408:46365:1756_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 1 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1408:40142:20681_1:N:0:TGTGACTG+AGCCTATC NW_026963341.1 122741 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1411:41607:2345_1:N:0:TGTGACTG+AGCCTATC NW_026963617.1 29271 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1411:41583:2359_1:N:0:TGTGACTG+AGCCTATC NW_026963617.1 29271 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1412:12709:7906_1:N:0:TGTGACTG+AGCCTATC NW_026963542.1 23756 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1429:34696:8956_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1429:34688:8970_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1429:34680:8984_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 2 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1436:49926:7892_1:N:0:TGTGACTG+AGCCTATC NW_026963586.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1436:49942:7892_1:N:0:CGTGACTG+AGCCTATC NW_026963586.1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1447:19426:6925_1:N:0:TGTGACTG+AGCCTATC NW_026963469.1 21276 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1451:13462:29268_1:N:0:TGTGACTG+AGCCTATC NW_026963422.1 18037 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1454:13276:29282_1:N:0:TGTGACTG+AGCCTATC NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1456:31119:21451_1:N:0:TGTGACTG+AGCCTATC NW_026963326.1 2 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1468:27478:16212_1:N:0:TGTGACTG+AGCCTATC NW_026963407.1 1 Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2105:12175:25780_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2110:4642:1028_1:N:0:TGTGACTG+AGCCTATC NW_026963402.1 95234 Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2119:12564:9727_1:N:0:TGTGACTG+AGCCTATC NW_026963365.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2125:36412:7780_1:N:0:TGTGACTG+AGCCTATC NW_026963657.1 17847 Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2153:3865:23553_1:N:0:TGTGACTG+AGCCTATC NW_026963340.1 4220804 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2159:46940:26284_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 2 Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2183:36930:1420_1:N:0:TGTGACTG+AGCCTATC NW_026963621.1 21441 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2187:39212:27951_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 2 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2193:8429:29492_1:N:0:TGTTACTG+AGCCTATC NW_026963566.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2195:51722:29716_1:N:0:GGTGACTG+NGCCTATC NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2197:36258:20709_1:N:0:TGTGACTG+AGCCTATC NW_026963711.1 23042 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2216:37326:19140_1:N:0:TGTGACTG+AGCCTATC NW_026963736.1 25932 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2218:50824:15890_1:N:0:TGTGACTG+AGCCTATC NW_026963305.1 1249883 Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2246:42626:11646_1:N:0:TGTGACTG+AGCATATC NW_026963339.1 277220 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2246:27648:25948_1:N:0:TGTGACTG+AGCCTATC NW_026963307.1 124900 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2250:27324:8074_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 3 Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2263:43152:27713_1:N:0:TGTGACTG+AGCCTATC NW_026963372.1 501131 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2295:13535:13033_1:N:0:TGTGACTG+AGCCTATC NW_026963630.1 20098 Processed 75000000 sequence pairs so far Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2324:41987:9279_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 2 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:28433:28707_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:28449:28707_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 2 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2336:4326:6337_1:N:0:TGTGACTG+AGCCTATC NW_026963639.1 24139 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2350:47190:3325_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2350:30302:24491_1:N:0:TGTGACTG+AGCCTATC NW_026963309.1 1 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2355:23877:23987_1:N:0:TGTGACTG+AGCCTATC NW_026963609.1 2 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2365:12046:20289_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 1 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2377:36047:10371_1:N:0:TGTGACTG+AGCCTATC NW_026963725.1 1 Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2395:31799:10161_1:N:0:TGTGACTG+AGCCTATC NW_026963347.1 1227509 Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2420:30820:7065_1:N:0:TGTGACTG+AGCCTATC NW_026963415.1 1 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2440:32147:2667_1:N:0:TGTGACTG+AGCCTATC NW_026963560.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2442:4779:9363_1:N:0:TGTGACTG+AGCCTATC NW_026963351.1 1 Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2446:17338:27209_1:N:0:TGTGACTG+AGCCTATC NW_026963305.1 2 Processed 92000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2462:5321:2821_1:N:0:TGTGACTG+AGCCTATC NW_026963413.1 32146 Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2475:43387:24645_1:N:0:TGTGACTG+AGCCTATC NW_026963307.1 124909 Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2487:26895:26298_1:N:0:TGTGACTG+AGCCTATC NW_026963463.1 1 Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2491:16319:10791_1:N:0:TGTGACTG+AGCATATC NW_026963308.1 1 Processed 97000000 sequence pairs so far 97080726 reads; of these: 97080726 (100.00%) were paired; of these: 39522426 (40.71%) aligned concordantly 0 times 17932108 (18.47%) aligned concordantly exactly 1 time 39626192 (40.82%) aligned concordantly >1 times 59.29% overall alignment rate 97080726 reads; of these: 97080726 (100.00%) were paired; of these: 39512470 (40.70%) aligned concordantly 0 times 17936108 (18.48%) aligned concordantly exactly 1 time 39632148 (40.82%) aligned concordantly >1 times 59.30% overall alignment rate Processed 97080726 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 388322904. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 388322904. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 388322904. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 388322904. Successfully deleted the temporary files 78M_R1.fastp-trim.fq.gz_C_to_T.fastq and 78M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 97080726 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2377302929 Total methylated C's in CpG context: 31711548 Total methylated C's in CHG context: 3496212 Total methylated C's in CHH context: 16093878 Total methylated C's in Unknown context: 394946 Total unmethylated C's in CpG context: 255189141 Total unmethylated C's in CHG context: 382380388 Total unmethylated C's in CHH context: 1688431762 Total unmethylated C's in Unknown context: 13107260 C methylated in CpG context: 11.1% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 2.9% Bismark completed in 0d 6h 43m 1s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe