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 /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ (absolute path is '/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code'): /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R1_001.fastp-trim.fq.gz /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R2_001.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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/output/14-Apul-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/8TB_HDD_03/sr320/github/timeseries_molecular/D-Apul/code Now reading in and storing sequence information of the genome specified in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 1A5_R1_001.fastp-trim.fq.gz to 1A5_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 1A5_R1_001.fastp-trim.fq.gz (42082754 sequences in total) Writing a G -> A converted version of the input file 1A5_R2_001.fastp-trim.fq.gz to 1A5_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 1A5_R2_001.fastp-trim.fq.gz (42082754 sequences in total) Input files are 1A5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A5_R2_001.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/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 1A5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A5_R2_001.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: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 77 * 0 0 * * 0 0 TGGATAGTAAGATATTTATTATTATAAGTTTTTTAATTATATTTTTTGAATTGTGTATGGTTTAAAAGGAAAGATTTGTATTTTATTAATTTTTTATTTAATTTTATTAGATAATT IIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-IIIIIIIIIIIIIIIIIIII YT:Z:UP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 141 * 0 0 * * 0 0 AATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCAAAAATCTTTCCAACTCTTTCCAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1A5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A5_R2_001.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: LH00526:197:22KFKVLT4:3:1101:51593:1056_1:N:0:AAGACCGT+CAATCGAC/1 83 ntLink_6_GA_converted 10288123 42 116M = 10288148 141 AATTATCTAATAAAATTAAATAAAAAATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCA IIIIIIIIIIIIIIIIIIII-IIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:109A6 YS:i:-6 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:51593:1056_2:N:0:AAGACCGT+CAATCGAC/2 163 ntLink_6_GA_converted 10288148 42 116M = 10288123 -141 AATTAATAAAATACAAATCTTTCCTTTTAAACCATACACAATTCAAAAAATATAATTAAAAAACTTATAATAATAAATATCTTACTATCCAAAAATCTTTCCAACTCTTTCCAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:84A31 YS:i:-6 YT:Z:CP >>> Writing bisulfite mapping results to 1A5_pe.bam <<< Reading in the sequence files /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/1A5_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1120:11374:9349_1:N:0:AAGACCGT+CAATCGAC ptg000066l 66411 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1128:8849:12066_1:N:0:AAGACCGT+CAATCGAC ptg000088l 96906 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1128:8841:12080_1:N:0:AAGACCGT+CAATCGAC ptg000088l 96906 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 LH00526:197:22KFKVLT4:3:1211:20154:5609_1:N:0:AAGACCGT+CAATCGAC ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1211:17994:11814_1:N:0:AAGACCGT+CAATCGAC ptg000116l 1 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1265:11609:2247_1:N:0:AAGACCGT+CAATCGAC ptg000121l 50737 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1303:41178:6421_1:N:0:AAGACCGT+CAATCGAC ptg000117l 30015 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1317:9141:18818_1:N:0:AAGACCGT+CAATCGAC ptg000115l 42049 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1330:21061:15358_1:N:0:AAGACCGT+CAATCGAC ptg000007l 12295855 Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1380:5426:9391_1:N:0:AAGACCGT+CAATCGAC ptg000146l 38990 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1388:30512:21045_1:N:0:AAGACCGT+CAATCGAC ptg000046l 2 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36007:7023_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36023:7023_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:35999:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36015:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1439:36031:7037_1:N:0:AAGACCGT+CAATCGAC ptg000117l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1442:2999:2667_1:N:0:AAGACCGT+CAATCGAC ptg000125l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1442:3007:2681_1:N:0:AAGACCGT+CAATCGAC ptg000125l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1442:3023:2681_1:N:0:AAGACCGT+CAATCGAC ptg000125l 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1473:20624:11184_1:N:0:AAGACCGT+CAATCGAC ptg000121l 50750 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1484:20276:4166_1:N:0:AAGACCGT+CAATCGAC ptg000120l 31326 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2115:16189:3675_1:N:0:AAGACCGT+CAATCGAC ptg000096l 2 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2178:45823:7009_1:N:0:AAGACCGT+CAATCGAC ptg000020l 17861296 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2185:25236:2079_1:N:0:AAGACCGT+CAATCGAC ptg000083l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2186:42408:10904_1:N:0:AAGACCGT+CAATCGAC ptg000082l 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2195:19151:23931_1:N:0:AAGACCGT+CAATCGAC ptg000083l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2207:28902:29324_1:N:0:AAGACCGT+CAATCGAC ptg000080l 40111 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:13511:10273_1:N:0:AAGACCGT+CAATCGAC ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:13527:10273_1:N:0:AAGACCGT+CAATCGAC ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2224:32835:2933_1:N:0:AAGACCGT+CAATCGAC ptg000046l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2232:22202:13327_1:N:0:AAGACCGT+CAATCGAC ptg000096l 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2251:45378:8620_1:N:0:AAGACCGT+CAATCGAC ptg000123l 44479 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2253:33604:9699_1:N:0:AAGACCGT+CAATCGAC ptg000090l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2253:33612:9713_1:N:0:AAGACCGT+CAATCGAC ptg000090l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2277:34680:29436_1:N:0:AAGACCGT+CAATCGAC ptg000124l 54853 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2286:18560:2317_1:N:0:AAGACCGT+CAATCGAC ptg000046l 39597 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2286:18576:2317_1:N:0:AAGACCGT+CAATCGAC ptg000046l 39597 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2286:18568:2331_1:N:0:AAGACCGT+CAATCGAC ptg000046l 39597 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2338:7984:18216_1:N:0:AAGACCGT+CAATCGAC ptg000077l 42495 Processed 18000000 sequence pairs so far Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2455:38079:21816_1:N:0:AAGACCGT+CAATCGAC ptg000107l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2455:38095:21816_1:N:0:AAGACCGT+CAATCGAC ptg000107l 1 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2490:18042:7332_1:N:0:AAGACCGT+CAATCGAC ptg000025l 2 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1130:28400:26634_1:N:0:AAGACCGT+CAATCGAC ptg000048l 1 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1133:50937:14489_1:N:0:AAGACCGT+CAATCGAC ptg000092l 28988 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1141:44115:25542_1:N:0:AAGACCGT+CAATCGAC ptg000082l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1141:44124:25556_1:N:0:AAGACCGT+CAATCGAC ptg000082l 2 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1166:47093:15932_1:N:0:AAGACCGT+CAATCGAC ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1166:47085:15946_1:N:0:AAGACCGT+CAATCGAC ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1193:22380:14812_1:N:0:AAGACCGT+CAATCGAC ptg000008l 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1228:41769:13551_1:N:0:AAGACCGT+CAATCGAC ptg000135l 25310 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1231:2270:17683_1:N:0:AAGACCGT+CAATCGAC ptg000039l 1 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1273:35999:14630_1:N:0:AAGACCGT+CAATCGAC ptg000048l 2 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1312:32414:18454_1:N:0:AAGACCGT+CAATCGAC ptg000066l 2 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1356:22388:16647_1:N:0:AAGACCGT+CAATCGAC ptg000093l 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1371:21457:7079_1:N:0:AAGACCGT+CAATCGAC ptg000048l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1375:11884:23735_1:N:0:AAGACCGT+CAATCGAC ptg000098l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1388:30731:11254_1:N:0:AAGACCGT+CAATCGAC ptg000105l 83227 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1424:40571:5959_1:N:0:AAGACCGT+CAATCGAC ptg000097l 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1462:9893:22278_1:N:0:AAGACCGT+CAATCGAC ptg000052l 52614 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1488:47377:24239_1:N:0:AAGACCGT+CAATCGAC ptg000045l 58007 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2101:24354:5230_1:N:0:AAGACCGT+CAATCGAC ptg000074l 12235 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2113:34300:6197_1:N:0:AAGACCGT+CAATCGAC ptg000092l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2127:38758:6603_1:N:0:AAGACCGT+CAATCGAC ptg000052l 52610 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2139:12483:1770_1:N:0:AAGACCGT+CAATCGAC ptg000008l 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2152:27777:29282_1:N:0:AAGACCGT+CAATCGAC ptg000075l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2152:27769:29296_1:N:0:AAGACCGT+CAATCGAC ptg000075l 1 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2194:33717:25444_1:N:0:AAGACCGT+CAATCGAC ptg000117l 29993 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2194:33733:25444_1:N:0:AAGACCGT+CAATCGAC ptg000117l 29993 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2209:39017:4614_1:N:0:AAGACCGT+CAATCGAC ptg000006l 3 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2219:28797:1939_1:N:0:AAGACCGT+CAATCGAC ptg000027l 16268248 Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2280:16966:11744_1:N:0:AAGACCGT+CAATCGAC ptg000093l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2288:12394:3241_1:N:0:AAGACCGT+CAATCGAC ptg000045l 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2320:25147:5987_1:N:0:AAGACCGT+CAATCGAC ptg000066l 66348 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2325:34607:24995_1:N:0:AAGACCGT+CAATCGAC ptg000065l 49682 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2372:30561:14237_1:N:0:AAGACCGT+CAATCGAC ptg000066l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2380:16942:6827_1:N:0:AAGACCGT+CAATCGAC ptg000016l 13007876 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2481:14765:18524_1:N:0:AAGACCGT+CAATCGAC ptg000048l 2 Processed 42000000 sequence pairs so far 42082754 reads; of these: 42082754 (100.00%) were paired; of these: 15361452 (36.50%) aligned concordantly 0 times 8523437 (20.25%) aligned concordantly exactly 1 time 18197865 (43.24%) aligned concordantly >1 times 63.50% overall alignment rate 42082754 reads; of these: 42082754 (100.00%) were paired; of these: 15384365 (36.56%) aligned concordantly 0 times 8517864 (20.24%) aligned concordantly exactly 1 time 18180525 (43.20%) aligned concordantly >1 times 63.44% overall alignment rate Processed 42082754 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 168331016. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 168331016. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 168331016. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 168331016. Successfully deleted the temporary files 1A5_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1A5_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 42082754 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1238765856 Total methylated C's in CpG context: 20451038 Total methylated C's in CHG context: 1223964 Total methylated C's in CHH context: 4997409 Total methylated C's in Unknown context: 64703 Total unmethylated C's in CpG context: 174045186 Total unmethylated C's in CHG context: 208121690 Total unmethylated C's in CHH context: 829926569 Total unmethylated C's in Unknown context: 3252706 C methylated in CpG context: 10.5% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.0% Bismark completed in 0d 2h 51m 51s ==================== Bismark run complete ====================