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/269M_R1.fastp-trim.fq.gz ../data/269M_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/269M_R1.fastp-trim.fq.gz and ../data/269M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 269M_R1.fastp-trim.fq.gz to 269M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 269M_R1.fastp-trim.fq.gz (96042449 sequences in total) Writing a G -> A converted version of the input file 269M_R2.fastp-trim.fq.gz to 269M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 269M_R2.fastp-trim.fq.gz (96042449 sequences in total) Input files are 269M_R1.fastp-trim.fq.gz_C_to_T.fastq and 269M_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 269M_R1.fastp-trim.fq.gz_C_to_T.fastq and 269M_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: LH00469:254:22HGFVLT4:2:1101:1138:1014_1:N:0:NGGCATGT+NGTCTTCA/1 99 NC_086373.1_CT_converted 113405425 42 131M = 113405438 144 AATAATATTTATAAGTTATTTTTTGTAATAATTTTATAGAGTTATATTTTTGATTGTTGTGAGAAAAATATTAAGAAAAAGTTATAAATATTTATTGAAGTGATTTTTTTAAATTATTTGTTTTAGTGATT IIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIII-IIII-IIII-IIIIIIII-IIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:8A122 YS:i:0 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1138:1014_2:N:0:NGGCATGT+NGTCTTCA/2 147 NC_086373.1_CT_converted 113405438 42 131M = 113405425 -144 AGTTATTTTTTGTAATAATTTTATAGAGTTATATTTTTGATTGTTGTGAGAAAAATATTAAGAAAAAGTTATAAATATTTATTGAAGTGATTTTTTTAAATTATTTGTTTTAGTGATTTTAAAAAGTTTGT IIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIII-III9IIIIIIIIIIIII-II9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIII 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 269M_R1.fastp-trim.fq.gz_C_to_T.fastq and 269M_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: LH00469:254:22HGFVLT4:2:1101:1138:1014_1:N:0:NGGCATGT+NGTCTTCA/1 83 NC_086378.1_GA_converted 88689521 0 71M3I12M5I5M3I7M1I9M5I10M = 88689508 -127 AATCACTAAAACAAATAATTTAAAAAAATCACTTCAATAAATATTTATAACTTTTTCTTAATATTTTTCTCACAACAATCAAAAATATAACTCTATAAAATTATTACAAAAAATAACTTATAAATATTATT IIIIIIIIIIIII-IIIIIIII-IIII-IIII-IIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-130 XN:i:0 XM:i:9 XO:i:5 XG:i:17 NM:i:26 MD:Z:16C60T3T2T1T14C6T0C2A1 YS:i:-104 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1138:1014_2:N:0:NGGCATGT+NGTCTTCA/2 163 NC_086378.1_GA_converted 88689508 0 84M3I12M5I5M3I13M1D6M = 88689521 127 ACAAACTTTTTAAAATCACTAAAACAAATAATTTAAAAAAATCACTTCAATAAATATTTATAACTTTTTCTTAATATTTTTCTCACAACAATCAAAAATATAACTCTATAAAATTATTACAAAAAATAACT IIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9II-IIIIIIIIIIIII9III-IIIII9IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIII AS:i:-104 XN:i:0 XM:i:8 XO:i:4 XG:i:12 NM:i:20 MD:Z:29C60T3T2T1T8A5^C1A2A1 YS:i:-130 YT:Z:CP >>> Writing bisulfite mapping results to 269M_pe.bam <<< Reading in the sequence files ../data/269M_R1.fastp-trim.fq.gz and ../data/269M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1125:40749:28343_1:N:0:TGGCATGT+CGTCTTCA NW_026963684.1 18467 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1135:11455:6939_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 3 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1157:27737:11730_1:N:0:TGGCATGT+CGTCTTCA NW_026963681.1 22774 Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1191:39098:3465_1:N:0:TGGCATGT+CGTCTTCA NW_026963506.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1191:9157:15932_1:N:0:TGGCATGT+CGTCTTCA NW_026963428.1 29820 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1205:10322:19939_1:N:0:TGGCATGT+CATCTTCA NW_026963632.1 20517 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1216:44989:20499_1:N:0:TGGCATGT+CGTCTTCA NW_026963484.1 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 LH00469:254:22HGFVLT4:2:1251:44431:16647_1:N:0:TGGCATGT+CGTCTTCA NW_026963347.1 1227508 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1265:4828:29338_1:N:0:TGGCATGT+CGTCTTCA NW_026963762.1 1 Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1282:28530:10357_1:N:0:TGGCATGT+CGTCTTCA NW_026963721.1 1 Processed 15000000 sequence pairs so far Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1306:32374:19700_1:N:0:TGGCATGT+CGTCTTCA NW_026963468.1 26871 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1317:47207:25430_1:N:0:TGGCATGT+CGTCTTCA NW_026963585.1 49257 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1329:45556:21283_1:N:0:TGGCATGT+CGTCTTCA NW_026963581.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1332:10589:19084_1:N:0:TGGCATGT+CGTCTTCA NW_026963582.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1336:38758:16409_1:N:0:TGGCATGT+CGTCTTCA NW_026963372.1 501127 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1342:8591:9965_1:N:0:TGGCATGT+CGTCTTCA NW_026963372.1 501141 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1344:27656:15400_1:N:0:TGGCATGT+CGTCTTCA NW_026963408.1 31988 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1352:15704:29254_1:N:0:TGGCATGT+CGTCTTCA NW_026963585.1 49254 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1352:15712:29268_1:N:0:TGGCATGT+CGTCTTCA NW_026963585.1 49254 Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1378:27575:10441_1:N:0:TGGCATGT+CGTCTTCA NW_026963711.1 22988 Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1388:39106:10819_1:N:0:TGGCATGT+CGTCTTCA NW_026963705.1 1 Processed 23000000 sequence pairs so far Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1410:43654:17151_1:N:0:TGGCATGT+CGTCTTCA NW_026963555.1 17665 Processed 25000000 sequence pairs so far Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1440:42821:11618_1:N:0:TGGCATGT+CGTCTTCA NW_026963771.1 24026 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1440:47012:20415_1:N:0:TGGCATGT+CGTCTTCA NW_026963585.1 49257 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 LH00469:254:22HGFVLT4:2:2102:5961:26676_1:N:0:TGGCATGT+CGTCTTCA NW_026963768.1 22294 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2157:38402:13187_1:N:0:TGGCATGT+CGTCTTCA NW_026963555.1 17674 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2175:34834:16983_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 3 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2179:18115:8130_1:N:0:TGGCATGT+CGTCTTCA NW_026963377.1 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2201:2667:7696_1:N:0:TGGCATGT+CGTCTTCA NW_026963632.1 20517 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2211:36282:28455_1:N:0:TGGCATGT+CGTCTTCA NW_026963684.1 18467 Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2232:16440:3185_1:N:0:TGGCATGT+CGTCTTCA NW_026963569.1 27450 Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2255:4245:1630_1:N:0:TGGCATGT+CGTCTTCA NW_026963333.1 249894 Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2292:43549:23637_1:N:0:TGGCATGT+CGTCTTCA NC_086374.1 103707520 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2292:43541:23651_1:N:0:TGGCATGT+CGTCTTCA NC_086374.1 103707520 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2292:43549:23665_1:N:0:TGGCATGT+CGTCTTCA NC_086374.1 103707520 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2296:46851:17781_1:N:0:TGGCATGT+CGTCTTCA NW_026963581.1 1 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far 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 LH00469:254:22HGFVLT4:2:2373:8793:22362_1:N:0:TGGCATGT+CGTCTTCA NW_026963575.1 32013 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2375:22752:17669_1:N:0:TGGCATGT+CGTCTTCA NW_026963719.1 1 Processed 52000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2386:45669:16156_1:N:0:TGGCATGT+CGTCTTCA NW_026963581.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2389:3824:9951_1:N:0:TGGCACGT+CGTCTTAA NW_026963609.1 25328 Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2406:29444:26816_1:N:0:TGGCATGT+CGTCTTCA NW_026963684.1 18467 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2429:34874:12767_1:N:0:TGGCATGT+CGTCTTCA NW_026963684.1 18467 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2442:18779:18047_1:N:0:TGGCATGT+CGTCTTCA NW_026963611.1 20013 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2446:31953:27012_1:N:0:TGGCATGT+CGTCTTCA NW_026963307.1 124884 Processed 57000000 sequence pairs so far Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2483:28910:1714_1:N:0:TGGCATGT+CGTCTTCA NW_026963581.1 1 Processed 59000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2490:14158:2429_1:N:0:TGGCATGT+CGTCTTCA NW_026963378.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2497:19297:5328_1:N:0:TGGCATGT+CGTCTTCA NW_026963291.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1103:8922:12865_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1109:16464:18300_1:N:0:TGGCATGT+CGTCTTCA NW_026963684.1 18466 Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1136:14150:9223_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1143:42392:26760_1:N:0:TGGCATGT+CGTCTTCA NW_026963564.1 19019 Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1153:22906:11828_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 1 Processed 62000000 sequence pairs so far Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1364:47037:17487_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 3 Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2282:50290:7906_1:N:0:TGGCATGT+CGTCTTAA NW_026963415.1 2 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2466:32552:19672_1:N:0:TGGCATGT+CGTCTTCA NW_026963437.1 1 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2487:36452:16423_1:N:0:TGGCATGT+CGTCTTCA NW_026963443.1 56358 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2487:18779:23539_1:N:0:TGGCATGT+CGTCTTCA NC_086380.1 80675421 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1280:33960:25079_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1280:33952:25093_1:N:0:TGGCATGT+CGTCTTCA NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1310:43678:19070_1:N:0:TGGCATGT+CGTCTTCA NW_026963333.1 249881 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1317:21255:21661_1:N:0:TGGCATGT+CGTCTTCA NW_026963372.1 501145 Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1375:23683:16843_1:N:0:TGGCATGT+CGTCTTCA NW_026963377.1 2 Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Processed 89000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2108:22283:16381_1:N:0:TGGCATGT+CGTCTTCA NW_026963585.1 49268 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2121:9885:24841_1:N:0:TGGCATGT+CGTCTTCA NW_026963335.1 3 Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2201:37755:9012_1:N:0:TGGCATGT+CGTCTTCA NW_026963319.1 249894 Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2450:28821:11282_1:N:0:TGGCATGT+CGTCTTCA NW_026963550.1 1 Processed 96000000 sequence pairs so far 96042449 reads; of these: 96042449 (100.00%) were paired; of these: 41043545 (42.73%) aligned concordantly 0 times 18917253 (19.70%) aligned concordantly exactly 1 time 36081651 (37.57%) aligned concordantly >1 times 57.27% overall alignment rate 96042449 reads; of these: 96042449 (100.00%) were paired; of these: 41050868 (42.74%) aligned concordantly 0 times 18917121 (19.70%) aligned concordantly exactly 1 time 36074460 (37.56%) aligned concordantly >1 times 57.26% overall alignment rate Processed 96042449 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 384169796. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 384169796. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 384169796. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 384169796. Successfully deleted the temporary files 269M_R1.fastp-trim.fq.gz_C_to_T.fastq and 269M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 96042449 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2319006670 Total methylated C's in CpG context: 29670979 Total methylated C's in CHG context: 3557126 Total methylated C's in CHH context: 16741494 Total methylated C's in Unknown context: 431202 Total unmethylated C's in CpG context: 236911489 Total unmethylated C's in CHG context: 366777505 Total unmethylated C's in CHH context: 1665348077 Total unmethylated C's in Unknown context: 13053776 C methylated in CpG context: 11.1% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.2% Bismark completed in 0d 6h 35m 37s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe