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/80M_R1.fastp-trim.fq.gz ../data/80M_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/80M_R1.fastp-trim.fq.gz and ../data/80M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 80M_R1.fastp-trim.fq.gz to 80M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 80M_R1.fastp-trim.fq.gz (91833544 sequences in total) Writing a G -> A converted version of the input file 80M_R2.fastp-trim.fq.gz to 80M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 80M_R2.fastp-trim.fq.gz (91833544 sequences in total) Input files are 80M_R1.fastp-trim.fq.gz_C_to_T.fastq and 80M_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 80M_R1.fastp-trim.fq.gz_C_to_T.fastq and 80M_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: LH00469:254:22HGFVLT4:2:1101:1397:1014_1:N:0:AGCACTTC+ACGTCCAA/1 77 * 0 0 * * 0 0 TTTTTTATGGTTTTTAAATTAAATTTATATAAAGTAATTTATATTAAATTAATTGAAATATTAAATTGTAATAAAAATATATTGTAGTAAAAATATATTTATTAAATTGATTAAAATAATTAATAATGTAT IIIIIIIIIIIIIII9IIIII9II-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9 YT:Z:UP LH00469:254:22HGFVLT4:2:1101:1397:1014_2:N:0:AGCACTTC+ACGTCCAA/2 141 * 0 0 * * 0 0 TTATTTTAATCAATTTAATAAATATATTTTTACTACAATATATTTTTATTACAATTTAATATTTCAATTAATTTAATATAAATTACTTTATATAAATTTAATTTAAAAACCATAAAAAACAAACAACTTAA IIIIIIIIII-I9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 80M_R1.fastp-trim.fq.gz_C_to_T.fastq and 80M_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: LH00469:254:22HGFVLT4:2:1101:1397:1014_1:N:0:AGCACTTC+ACGTCCAA/1 83 NC_086375.1_GA_converted 75639756 42 131M = 75639768 143 ATACATTATTAATTATTTTAATCAATTTAATAAATATATTTTTACTACAATATATTTTTATTACAATTTAATATTTCAATTAATTTAATATAAATTACTTTATATAAATTTAATTTAAAAACCATAAAAAA 9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-II9IIIII9IIIIIIIIIIIIIII AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:0C8C27C59A33 YS:i:-18 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1397:1014_2:N:0:AGCACTTC+ACGTCCAA/2 163 NC_086375.1_GA_converted 75639768 42 131M = 75639756 -143 TTATTTTAATCAATTTAATAAATATATTTTTACTACAATATATTTTTATTACAATTTAATATTTCAATTAATTTAATATAAATTACTTTATATAAATTTAATTTAAAAACCATAAAAAACAAACAACTTAA IIIIIIIIII-I9III9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII-9IIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:25C59A33T11 YS:i:-24 YT:Z:CP >>> Writing bisulfite mapping results to 80M_pe.bam <<< Reading in the sequence files ../data/80M_R1.fastp-trim.fq.gz and ../data/80M_R2.fastp-trim.fq.gz Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1107:5896:12080_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1107:5888:12094_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1107:5904:12094_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1107:5896:12108_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 2 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1115:29557:11744_1:N:0:AGCACTTC+ACGTCCAA NW_026963585.1 2 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:17775:17235_1:N:0:AGCACTTC+ACGTCCAA NW_026963314.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:17791:17235_1:N:0:AGCACTTC+ACGTCCAA NW_026963314.1 1 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1137:31427:20527_1:N:0:AGCACTTC+ACGTCCAA NW_026963305.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1137:31443:20527_1:N:0:AGCACTTC+ACGTCCAA NW_026963305.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1138:47368:12486_1:N:0:AGCACTTC+ACGTCCAA NW_026963543.1 22018 Processed 4000000 sequence pairs so far Processed 5000000 sequence pairs so far Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1189:49084:22152_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 1 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1215:1146:21339_1:N:0:AGCACTTC+ACGTCCAA NW_026963661.1 19673 Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1235:25552:1504_1:N:0:AGCACTTC+ACGTCCAA NW_026963378.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1236:40660:15694_1:N:0:AGCACTTC+ACGTCCAA NW_026963585.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1254:48825:4670_1:N:0:AGCACTTC+ACGTCCAA NC_086374.1 103707533 Processed 16000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1268:3444:1953_1:N:0:AGCACTTC+ACGTCAAA NW_026963712.1 2 Processed 17000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1272:11390:27447_1:N:0:AGCACTTC+ACGTCCAA NW_026963634.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1272:11407:27447_1:N:0:AGCACTTC+ACGTCCAA NW_026963634.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1274:23683:18272_1:N:0:AGCACTTC+ACGTCCAA NW_026963399.1 2 Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1282:42173:9321_1:N:0:AGCACTTC+ACGTCCAA NW_026963422.1 18034 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1286:38111:19714_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 1 Processed 19000000 sequence pairs so far Processed 20000000 sequence pairs so far Processed 21000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1323:8154:3746_1:N:0:AGCACTTC+ACGTCCAA NW_026963611.1 2 Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1334:51398:27895_1:N:0:AGCACTTC+ACGTCCAA NW_026963743.1 1 Processed 24000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1351:37553:12164_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 3 Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1363:41663:10455_1:N:0:AGCACTTC+ACGTCCAA NW_026963500.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1364:12337:24603_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 1 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1366:12094:13257_1:N:0:AGCACTTC+ACGTCCAA NW_026963581.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1374:10379:14209_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 1 Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1381:25787:6225_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 56338 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1394:18253:22040_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 2 Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1448:23683:24127_1:N:0:AGCACTTC+ACGTCCAA NW_026963634.1 1 Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1452:26385:25500_1:N:0:AGCACTTC+ACGTCCAA NW_026963661.1 19652 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1454:46527:12795_1:N:0:AGCACTTC+ACGTCCAA NW_026963590.1 22589 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1458:31896:8200_1:N:0:AGCACTTC+ACGTCCAA NW_026963418.1 2 Processed 35000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1460:20170:11492_1:N:0:AGCACTTC+ACGTCCAA NW_026963585.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1460:44941:19658_1:N:0:AGCACTTC+ACGTCCAA NW_026963516.1 2 Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1471:17541:24197_1:N:0:AGCACTTC+ACGTCCAA NW_026963418.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1471:17532:24211_1:N:0:AGCACTTC+ACGTCCAA NW_026963418.1 2 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1490:7134:26914_1:N:0:AGCACTTC+ACGTCCAA NW_026963342.1 58182 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2101:37812:22950_1:N:0:AGCACTTC+ACGTCCAA NW_026963303.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2101:37828:22950_1:N:0:AGCACTTC+ACGTCCAA NW_026963303.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2104:46705:2905_1:N:0:AGCACTTC+ACGTCCAA NW_026963377.1 2 Processed 39000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2114:29905:24141_1:N:0:AGCACTTC+ACGTCCAA NW_026963585.1 2 Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2125:43678:27839_1:N:0:AGCACTTC+ACGTCCAA NW_026963598.1 3 Processed 42000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2140:22752:7836_1:N:0:AGCACTTC+ACGTCCAA NC_086385.1 2 Processed 43000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2151:9027:8648_1:N:0:AGCACTTC+ACGTCCAA NW_026963771.1 24029 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2152:37609:9657_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2154:24039:18216_1:N:0:AGCACTTC+ACGTCCAA NW_026963596.1 1 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far 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 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2272:18398:19042_1:N:0:AGCACTTC+ACGTCCAA NW_026963781.1 28294 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2282:32851:7135_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 56352 Processed 56000000 sequence pairs so far Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2304:12871:19392_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 3 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 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2360:30529:4684_1:N:0:AGCACTTC+ACGTCCAA NW_026963293.1 3 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2365:47547:25626_1:N:0:AGCACTTC+ACGTCCAA NW_026963618.1 25613 Processed 63000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2377:4698:3339_1:N:0:AGCACTTC+ACGTCCAA NW_026963299.1 2 Processed 64000000 sequence pairs so far Processed 65000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2394:46770:11674_1:N:0:AGCACTTC+ACGTCCAA NW_026963372.1 501153 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2397:1453:24953_1:N:0:AGCACTTC+ACGTCCAA NW_026963319.1 249875 Processed 66000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2407:19232:7205_1:N:0:AGCACTTC+ACGTCCAA NW_026963812.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2407:19248:7205_1:N:0:AGCACTTC+ACGTCCAA NW_026963721.1 2 Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2435:27033:22810_1:N:0:AGCACTTC+ACGTCCAA NW_026963771.1 24029 Processed 69000000 sequence pairs so far Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2459:42367:27671_1:N:0:AGCACTTC+ACGTCCAA NW_026963576.1 2 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 LH00586:122:22HTFTLT4:7:1140:45977:17697_1:N:0:AGCACTTC+ACGTCCAA NW_026963308.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1177:37488:21157_1:N:0:AGCACTTC+ACGTCCAA NW_026963319.1 249902 Processed 76000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1219:51884:10441_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 2 Processed 77000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1225:46252:6631_1:N:0:AGCACTTC+ACGTCCAA NW_026963415.1 2 Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1340:43144:15792_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 56348 Processed 80000000 sequence pairs so far Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1405:4690:23048_1:N:0:AGCACTTC+ACGTCCAA NW_026963585.1 2 Processed 82000000 sequence pairs so far Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2231:31815:7191_1:N:0:AGCAATTC+ACGTCCAA NW_026963307.1 124915 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2262:45572:2513_1:N:0:AGCACTTC+ACGTCCAA NW_026963443.1 56352 Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2286:29744:8060_1:N:0:AGCACTTC+ACGACCAA NW_026963347.1 1227486 Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2363:6551:6967_1:N:0:AGCACTTC+ACGTCCAA NW_026963361.1 2 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far 91833544 reads; of these: 91833544 (100.00%) were paired; of these: 38252864 (41.65%) aligned concordantly 0 times 17554001 (19.12%) aligned concordantly exactly 1 time 36026679 (39.23%) aligned concordantly >1 times 58.35% overall alignment rate 91833544 reads; of these: 91833544 (100.00%) were paired; of these: 38247167 (41.65%) aligned concordantly 0 times 17555618 (19.12%) aligned concordantly exactly 1 time 36030759 (39.23%) aligned concordantly >1 times 58.35% overall alignment rate Processed 91833544 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 367334176. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 367334176. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 367334176. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 367334176. Successfully deleted the temporary files 80M_R1.fastp-trim.fq.gz_C_to_T.fastq and 80M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 91833544 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2248265980 Total methylated C's in CpG context: 31402349 Total methylated C's in CHG context: 3448138 Total methylated C's in CHH context: 15900992 Total methylated C's in Unknown context: 407356 Total unmethylated C's in CpG context: 235871610 Total unmethylated C's in CHG context: 360092158 Total unmethylated C's in CHH context: 1601550733 Total unmethylated C's in Unknown context: 12487953 C methylated in CpG context: 11.7% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.2% Bismark completed in 0d 6h 20m 35s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe