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/241M_R1.fastp-trim.fq.gz ../data/241M_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/241M_R1.fastp-trim.fq.gz and ../data/241M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 241M_R1.fastp-trim.fq.gz to 241M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 241M_R1.fastp-trim.fq.gz (86216365 sequences in total) Writing a G -> A converted version of the input file 241M_R2.fastp-trim.fq.gz to 241M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 241M_R2.fastp-trim.fq.gz (86216365 sequences in total) Input files are 241M_R1.fastp-trim.fq.gz_C_to_T.fastq and 241M_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 241M_R1.fastp-trim.fq.gz_C_to_T.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 99 NC_086385.1_CT_converted 15645290 42 131M = 15645303 144 AATTTGTTGTTAATTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAG IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9A121 YS:i:0 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 147 NC_086385.1_CT_converted 15645303 42 131M = 15645290 -144 TTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAGATATGGGTTTTGA IIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIII9IIII9IIIIIIIII-9IIIII9 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:131 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 241M_R1.fastp-trim.fq.gz_C_to_T.fastq and 241M_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: LH00469:254:22HGFVLT4:2:1101:3581:1014_1:N:0:TTGCGAAG+AACACGCT/1 77 * 0 0 * * 0 0 AATTTGTTGTTAATTAAGAAATTAAGTATTATGAATATGTTATTTTTAGAGAATTTTTTGATTAAATAAGAATGTATTTTTATAAGTTATGAATAAAATTTTTTTTAAAAATAGATGTAGTTTGTTATGAG IIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP LH00469:254:22HGFVLT4:2:1101:3581:1014_2:N:0:TTGCGAAG+AACACGCT/2 141 * 0 0 * * 0 0 TCAAAACCCATATCTCATAACAAACTACATCTATTTTTAAAAAAAATTTTATTCATAACTTATAAAAATACATTCTTATTTAATCAAAAAATTCTCTAAAAATAACATATTCATAATACTTAATTTCTTAA 9IIIII9-IIIIIIIII9IIII9IIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIII YT:Z:UP >>> Writing bisulfite mapping results to 241M_pe.bam <<< Reading in the sequence files ../data/241M_R1.fastp-trim.fq.gz and ../data/241M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1118:18665:14826_1:N:0:TTGCGAAG+AACACGCT NW_026963369.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1122:42513:15260_1:N:0:TTGCGAAG+AACACGCT NW_026963365.1 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1127:24200:23791_1:N:0:TTGCGAAG+AACACGCT NW_026963303.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1131:11997:20849_1:N:0:TTGCGAAG+AACACGCT NW_026963299.1 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1142:16149:22096_1:N:0:TTGCGAAG+AACACGCT NW_026963372.1 501128 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1158:14465:24981_1:N:0:TTGCGAAG+AACACGCT NW_026963738.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1215:42270:5034_1:N:0:TTGCGAAG+AACACGCT NW_026963393.1 1 Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1239:49869:19056_1:N:0:CTGCGAAG+AACACGCT NW_026963616.1 36413 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1257:28684:8298_1:N:0:TTGCGAAG+AACACGCT NW_026963592.1 19027 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1261:30310:17557_1:N:0:TTGCGAAG+AACACGCC NW_026963468.1 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1296:15469:12879_1:N:0:TTGCGAAG+AACACGCT NW_026963663.1 21843 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1301:45289:9139_1:N:0:TTGCGAAG+AACACGCT NC_086376.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1302:23294:20625_1:N:0:TTGCGAAG+AACACGCT NW_026963335.1 1 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1319:51560:2513_1:N:0:TTGCGAAG+AACACGCT NW_026963348.1 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1342:46859:18972_1:N:0:TTGCGAAG+AACACGCT NW_026963307.1 124893 Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1346:39123:11660_1:N:0:TTGCGAAG+AACACGCT NW_026963739.1 19671 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1375:51172:10581_1:N:0:TTGCGAAG+AACACGCT NW_026963741.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1386:36816:9321_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1392:46940:24827_1:N:0:TTGCGAAG+AACACGCT NW_026963680.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1401:1227:8032_1:N:0:TTGCGAAG+AACACGCT NW_026963299.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1416:13252:4782_1:N:0:TTGCGAAG+AACACGCT NW_026963418.1 1 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1453:37043:23777_1:N:0:TTGCGAAG+AACACGCT NW_026963720.1 20495 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1462:41566:24071_1:N:0:TTGCGAAG+AACACGCT NW_026963413.1 32164 Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1487:19313:19532_1:N:0:TTGCGAAG+AACACGCT NC_007687.1 18544 Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1496:14935:6295_1:N:0:TTGCGAAG+AACACGCT NW_026963307.1 124890 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2126:11941:15092_1:N:0:TTGCGAAG+AACACGCT NW_026963762.1 14846 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2132:17969:24575_1:N:0:TTGCGAAG+AACACGCT NW_026963393.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2137:4965:2709_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18482 Processed 37000000 sequence pairs so far Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2153:19831:16030_1:N:0:TTGCGAAG+AACACGTT NW_026963583.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2160:37132:27096_1:N:0:TTGCGAAG+AACACGCT NW_026963348.1 1 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2177:17654:3802_1:N:0:TTGCGAAG+AACACGCT NW_026963608.1 22013 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2185:25333:8354_1:N:0:TTGCGAAG+AACACGCT NW_026963291.1 1 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2219:51730:11660_1:N:0:TTGCGAAG+AACACGCT NW_026963786.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2226:25269:18944_1:N:0:TTGCGAAG+AACACGCT NW_026963709.1 24958 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2226:25285:18944_1:N:0:TTGCGAAG+AACACGCT NW_026963709.1 24958 Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2236:3929:9685_1:N:0:TTGCGAAG+AACACGCT NW_026963598.1 29345 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2243:11075:5525_1:N:0:TTGCGAAG+AACACGCT NW_026963771.1 24026 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2248:47417:4838_1:N:0:TTGCGAAG+AACACGCT NC_007687.1 18560 Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2261:49222:23791_1:N:0:TTGCGAAG+AACACGCT NW_026963415.1 2 Processed 47000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2267:48412:12360_1:N:0:TTGCGAAG+AACACGCT NW_026963608.1 22011 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2270:35230:20359_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18060 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2270:35246:20359_1:N:0:TTGCGAAG+AACACGCT NW_026963422.1 18060 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2271:33320:25346_1:N:0:TTGCGAAG+AACACGCT NW_026963586.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2271:33345:25360_1:N:0:TTGCGAAG+AACACGCT NW_026963586.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2271:33353:25374_1:N:0:TTGCGAAG+AACACGCT NW_026963586.1 1 Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2323:43881:21858_1:N:0:TTGCGAAG+AACACGCT NW_026963592.1 1 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2333:39932:24463_1:N:0:TTGCGAAG+AACACGCT NW_026963776.1 2 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2344:41016:22642_1:N:0:TTGCGAAG+AACACGCT NW_026963415.1 2 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2376:9578:15764_1:N:0:TTGCGAAG+AACACGCT NW_026963598.1 29339 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2383:35610:2275_1:N:0:TTGCGAAG+AACACACT NW_026963612.1 23744 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2490:10703:11576_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2490:13171:19266_1:N:0:TTGCGAAG+AACACGCT NW_026963757.1 32613 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2491:38702:7346_1:N:0:TTGCGAAG+AACACGCT NW_026963345.1 224368 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1173:47255:24925_1:N:0:TTGCGAAG+AACACGCT NW_026963299.1 1 Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1198:27154:10245_1:N:0:TTGCGAAG+AACACGCT NW_026963291.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1202:33984:24141_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18465 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1212:17015:13509_1:N:0:TTGCGAAG+AACACGCT NW_026963804.1 1 Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1235:17791:25051_1:N:0:TTGCGAAG+AACACGCT NW_026963576.1 1 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1327:2513:19700_1:N:0:TTGCGAAG+AACACGCT NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1345:34955:9265_1:N:0:TTGCGAAG+AACACGCT NW_026963598.1 29322 Processed 72000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1380:14846:10203_1:N:0:TTGCGAAG+AACACGCT NW_026963372.1 501149 Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far 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 LH00586:122:22HTFTLT4:7:2150:9553:17991_1:N:0:TTGCGAAG+AACACGCT NW_026963307.1 124894 Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2221:12216:11590_1:N:0:TTGCGAAG+AACACGCT NW_026963415.1 2 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2235:30529:10007_1:N:0:TTGCGAAG+AACACGCT NW_026963743.1 1 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2374:48210:4194_1:N:0:TTGCGAAG+AACACGCT NW_026963415.1 1 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2392:48833:3647_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18473 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2401:6600:28819_1:N:0:TTGCGAAG+AACACGCT NW_026963743.1 1 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2438:37480:4278_1:N:0:TTGCGAAG+AACACGCT NW_026963684.1 18480 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2447:25989:13299_1:N:0:TTGCGAAG+AACACGCT NW_026963631.1 26249 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far 86216365 reads; of these: 86216365 (100.00%) were paired; of these: 34421561 (39.92%) aligned concordantly 0 times 16196523 (18.79%) aligned concordantly exactly 1 time 35598281 (41.29%) aligned concordantly >1 times 60.08% overall alignment rate 86216365 reads; of these: 86216365 (100.00%) were paired; of these: 34429991 (39.93%) aligned concordantly 0 times 16186871 (18.77%) aligned concordantly exactly 1 time 35599503 (41.29%) aligned concordantly >1 times 60.07% overall alignment rate Processed 86216365 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 344865460. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 344865460. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 344865460. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 344865460. Successfully deleted the temporary files 241M_R1.fastp-trim.fq.gz_C_to_T.fastq and 241M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 86216365 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2148641040 Total methylated C's in CpG context: 28559486 Total methylated C's in CHG context: 3281483 Total methylated C's in CHH context: 15167758 Total methylated C's in Unknown context: 383076 Total unmethylated C's in CpG context: 231620176 Total unmethylated C's in CHG context: 347187776 Total unmethylated C's in CHH context: 1522824361 Total unmethylated C's in Unknown context: 11907053 C methylated in CpG context: 11.0% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.1% Bismark completed in 0d 6h 0m 31s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe