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/1C9_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/1C9_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/1C9_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/1C9_R2_001.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 1C9_R1_001.fastp-trim.fq.gz to 1C9_R1_001.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 1C9_R1_001.fastp-trim.fq.gz (40660437 sequences in total) Writing a G -> A converted version of the input file 1C9_R2_001.fastp-trim.fq.gz to 1C9_R2_001.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 1C9_R2_001.fastp-trim.fq.gz (40660437 sequences in total) Input files are 1C9_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1C9_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 1C9_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 99 ntLink_6_CT_converted 9891496 0 44M11D81M = 9891483 -149 TGTAATATGGGTAGATATTTTTTTGTTAAGGGAGTTGGAGGATGTTAAGGTATTTGAAGGAATTAATATAGTTTAGGATTTTGTTGTTAATTTTGATTTTAGGTGTATTGGTTGTGGATTTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-61 XN:i:0 XM:i:1 XO:i:1 XG:i:11 NM:i:12 MD:Z:44^ATAGGTTGTTT9G71 YS:i:-44 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 147 ntLink_6_CT_converted 9891483 0 57M11D68M = 9891496 149 AGGTATTTGTTTTTGTAATATGGGTAGATATTTTTTTGTTAAGGGAGTTGGAGGATGTTAAGGTATTTGAAGGAATTAATATAGTTTAGGATTTTGTTGTTAATTTTGATTTTAGGTGTATTGGT IIII-IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-44 XS:i:-61 XN:i:0 XM:i:1 XO:i:1 XG:i:11 NM:i:12 MD:Z:57^ATAGGTTGTTT9G58 YS:i:-44 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 1C9_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1C9_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: LH00526:197:22KFKVLT4:3:1101:49456:1056_1:N:0:TCCTCATG+AGGTGTAC/1 83 ptg000018l_GA_converted 10448679 2 81M11D44M = 10448692 149 AAAAAAATCCACAACCAATACACCTAAAATCAAAATTAACAACAAAATCCTAAACTATATTAATTCCTTCAAATACCTTAACATCCTCCAACTCCCTTAACAAAAAAATATCTACCCATATTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-56 XS:i:-68 XN:i:0 XM:i:3 XO:i:1 XG:i:11 NM:i:14 MD:Z:15T55C9^AAACAACCTAT13T30 YS:i:-56 YT:Z:CP LH00526:197:22KFKVLT4:3:1101:49456:1056_2:N:0:TCCTCATG+AGGTGTAC/2 163 ptg000018l_GA_converted 10448692 2 68M11D57M = 10448679 -149 ACCAATACACCTAAAATCAAAATTAACAACAAAATCCTAAACTATATTAATTCCTTCAAATACCTTAACATCCTCCAACTCCCTTAACAAAAAAATATCTACCCATATTACAAAAACAAATACCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII-IIII AS:i:-56 XS:i:-62 XN:i:0 XM:i:3 XO:i:1 XG:i:11 NM:i:14 MD:Z:2T55C9^AAACAACCTAT13T43 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 1C9_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/1C9_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/1C9_R2_001.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1113:1364:3535_1:N:0:TCCTCATG+AGGTGTAC ptg000012l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1124:7943:6743_1:N:0:TCCTCATG+AGGTGTAC ptg000092l 2 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1138:30933:17011_1:N:0:TCCTCATG+AGGTGTAC ptg000105l 83250 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1185:36986:27629_1:N:0:TCCTCATG+AGGTGTAC ptg000012l 1 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1248:24856:15624_1:N:0:TCCTCATG+AGGTGTAC ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1259:43039:2023_1:N:0:TCCTCATG+AGGTGTAC ptg000117l 30010 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1259:43047:2037_1:N:0:TCCTCATG+AGGTGTAC ptg000117l 30010 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1288:47805:11254_1:N:0:TCCTCATG+AGGTGTAC ptg000106l 40384 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1319:41574:5062_1:N:0:TCCTCATG+AGGTGTAC ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1324:19369:20191_1:N:0:TCCTCATG+AGGTGTAC ptg000019l 6029769 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1339:17799:7892_1:N:0:TCCTCATG+AGGTGTAC ptg000129l 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1374:34737:23342_1:N:0:TCCTCATG+AGGTGTAC ptg000066l 66350 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1425:47118:9755_1:N:0:TCCTCATG+AGGTGTAC ptg000113l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1434:8760:27321_1:N:0:TCCTCATG+AGGTGTAC ptg000066l 66411 Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1460:40976:23749_1:N:0:TCCTCATG+AGGTGTAC ptg000114l 51140 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:1462:12807:28021_1:N:0:TCCTCATG+AGGTGTAC ptg000046l 1 Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2208:15687:22418_1:N:0:TCCTCATG+AGGTGTAC ptg000115l 42069 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2210:13017:3844_1:N:0:TCCTCATG+AGGTGTAC ptg000066l 66345 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2320:48971:14391_1:N:0:TCCTCATG+AGGTGTAC ptg000019l 6029774 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2370:25997:14377_1:N:0:TCCTCATG+AGGTGTAC ntLink_4 304032 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2379:17168:9937_1:N:0:TCCTCATG+AGGTGTAC ptg000075l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2385:22962:18005_1:N:0:TCCTCATG+AGGTGTAC ptg000096l 56413 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2403:21846:15820_1:N:0:TCCTCATG+AGGTGTAC ptg000155l 36785 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2408:9756:8648_1:N:0:TCCTCATG+AGGTGTAC ptg000109l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2408:9748:8662_1:N:0:TCCTCATG+AGGTGTAC ptg000109l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2423:29161:15036_1:N:0:TCCTCATG+AGGTGTAC ptg000133l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2423:29153:15050_1:N:0:TCCTCATG+AGGTGTAC ptg000133l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2423:29169:15050_1:N:0:TCCTCATG+AGGTGTAC ptg000133l 2 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2490:25188:21325_1:N:0:TCCTCATG+AGGTGTAC ptg000121l 50745 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:3:2490:25180:21339_1:N:0:TCCTCATG+AGGTGTAC ptg000121l 50745 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1105:48679:17053_1:N:0:TCCTCATG+AGGTGTAC ptg000113l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1114:24759:6099_1:N:0:TCCTCATG+AGGTGTAC ptg000092l 28992 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1159:24783:6421_1:N:0:TCCTCATG+AGGTGTAC ptg000096l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1164:7425:8312_1:N:0:TCCTCATG+AGGTGTAC ptg000160l 32584 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1164:7417:8326_1:N:0:TCCTCATG+AGGTGTAC ptg000117l 29995 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1168:43468:14924_1:N:0:TCCTCATG+AGGTGTAC ptg000174l 27225 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1174:18487:13145_1:N:0:TCCTCATG+AGGTGTAC ptg000057l 39960 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1201:27162:21465_1:N:0:TCCTCATG+AGGTGTAC ptg000116l 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1228:31014:17123_1:N:0:TCCTCATG+AGGTGTAC ptg000045l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1229:18495:28511_1:N:0:TCCTCATG+AGGTGTAC ptg000012l 20102961 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1248:14223:24729_1:N:0:TCCTCATG+AGGTGTAC ptg000048l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1252:4561:9573_1:N:0:TCCTCATG+AGGTGTAC ptg000129l 33365 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1308:42643:2849_1:N:0:TCCTCATG+AGGTGTAC ptg000012l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1317:35635:14111_1:N:0:TCCTCATG+AGGTGTAC ntLink_4 304029 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1325:17694:20289_1:N:0:TCCTCATG+AGGTGTAC ptg000048l 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1332:51957:25696_1:N:0:TCCTCATG+AGGTGTAC ptg000094l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1335:42537:22054_1:N:0:TCCTCATG+AGGTGTAC ptg000092l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1335:41453:28946_1:N:0:TCCTCATG+AGGTGTAC ptg000066l 66411 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1369:3743:27657_1:N:0:TCCTCATG+AGGTGTAC ptg000020l 17861296 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1452:45224:4180_1:N:0:TCCTCATG+AGGTGTAC ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1452:45232:4194_1:N:0:TCCTCATG+AGGTGTAC ptg000097l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1452:14085:18047_1:N:0:TCCTCATG+AGGTGTAC ptg000066l 1 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:1463:22647:22194_1:N:0:TCCTCATG+AGGTGTAC ptg000121l 50746 Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2121:24200:22334_1:N:0:TCCTCATG+AGGTGTAC ptg000106l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2121:24209:22348_1:N:0:TCCTCATG+AGGTGTAC ptg000106l 2 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2148:11601:6883_1:N:0:TCCTCATG+AGGTGTAC ptg000006l 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2188:12887:21914_1:N:0:TCCTCATG+AGGTGTAC ptg000033l 2625611 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2198:14433:2653_1:N:0:TCCTCATG+AGGTGTAC ptg000024l 2 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2206:39778:25878_1:N:0:TCCTCATG+AGGTGTAC ptg000063l 30363 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2243:28020:11604_1:N:0:TCCTCATG+AGGTGTAC ptg000184l 44409 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2243:28036:11604_1:N:0:TCCTCATG+AGGTGTAC ptg000184l 44409 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2273:10055:23118_1:N:0:TCCTCATG+AGGTGTAC ptg000046l 39601 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2289:49950:5244_1:N:0:TCCTCATG+AGGTGTAC ptg000083l 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2350:4941:1742_1:N:0:TCCTCATG+AGGTGTAC ptg000075l 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2398:48291:27363_1:N:0:TCCTCATG+AGGTGTAC ptg000024l 1 Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2420:32932:22124_1:N:0:TCCTCATG+AGGTGTAC ptg000129l 33360 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00526:197:22KFKVLT4:4:2448:30480:13537_1:N:0:TCCTCATG+AGGTGTAC ptg000082l 1 Processed 40000000 sequence pairs so far 40660437 reads; of these: 40660437 (100.00%) were paired; of these: 15780349 (38.81%) aligned concordantly 0 times 8706962 (21.41%) aligned concordantly exactly 1 time 16173126 (39.78%) aligned concordantly >1 times 61.19% overall alignment rate 40660437 reads; of these: 40660437 (100.00%) were paired; of these: 15766464 (38.78%) aligned concordantly 0 times 8710592 (21.42%) aligned concordantly exactly 1 time 16183381 (39.80%) aligned concordantly >1 times 61.22% overall alignment rate Processed 40660437 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 162641748. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 162641748. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 162641748. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 162641748. Successfully deleted the temporary files 1C9_R1_001.fastp-trim.fq.gz_C_to_T.fastq and 1C9_R2_001.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 40660437 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1258109099 Total methylated C's in CpG context: 23530589 Total methylated C's in CHG context: 1306063 Total methylated C's in CHH context: 5269937 Total methylated C's in Unknown context: 67857 Total unmethylated C's in CpG context: 171379831 Total unmethylated C's in CHG context: 212511581 Total unmethylated C's in CHH context: 844111098 Total unmethylated C's in Unknown context: 3113329 C methylated in CpG context: 12.1% C methylated in CHG context: 0.6% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.1% Bismark completed in 0d 2h 53m 35s ==================== Bismark run complete ====================