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/270M_R1.fastp-trim.fq.gz ../data/270M_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/270M_R1.fastp-trim.fq.gz and ../data/270M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 270M_R1.fastp-trim.fq.gz to 270M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 270M_R1.fastp-trim.fq.gz (99002878 sequences in total) Writing a G -> A converted version of the input file 270M_R2.fastp-trim.fq.gz to 270M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 270M_R2.fastp-trim.fq.gz (99002878 sequences in total) Input files are 270M_R1.fastp-trim.fq.gz_C_to_T.fastq and 270M_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 270M_R1.fastp-trim.fq.gz_C_to_T.fastq and 270M_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: LH00469:254:22HGFVLT4:2:1101:1639:1014_1:N:0:CTGTTAAC+ACCTCAGT/1 99 NC_086382.1_CT_converted 15181713 1 131M = 15181857 274 TATTTGGGGTATTATGTGTAATTATTTTTTTATAGGTTGTTATGGTAAAGTTTTTTTTTGTTGTTTAGTTTATATTATAATTTTGTATATGTATGATGGTTTGTTTTGAAGTTGAGATATTTTTATATATG IIIIIIIIIIIII-IIIII-9I9II9I9IIIIII9IIII9--IIII--II-III9I-II9IIII9999II9III9IIIII-I9IIIIIIIII9II-I9II9II9I999I-I9IIIIIIII9III99I9I-9 AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:40A39A50 YS:i:-14 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1639:1014_2:N:0:CTGTTAAC+ACCTCAGT/2 147 NC_086382.1_CT_converted 15181857 1 4M1I126M = 15181713 -274 TGGGTGTATGAAGTGTGATTTATTTTTTTGTAATTTAGTAAATTTAGAGTATTTTTTTGTGATGTGGTTTTTTGTGGTAAAAAATTTTATTTTTAATATAATAAGTTTGTTGAAATTTTAATATTTTGAAT IIIIIIIIII9IIIIIIIIII9IIII9IIIIIII9III9III9IIIIII9II--IIIIIIIIIIII99I9IIIIIIIII9IIIIIIIIIIIII-IIII9IIIIIIII9III9IIIIIIIIIIIIIIIII-I AS:i:-14 XS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:72A57 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 270M_R1.fastp-trim.fq.gz_C_to_T.fastq and 270M_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: LH00469:254:22HGFVLT4:2:1101:1639:1014_1:N:0:CTGTTAAC+ACCTCAGT/1 83 NW_026963318.1_GA_converted 2256571 1 46M1I84M = 2256429 -272 CATATATAAAAATATCTCAACTTCAAAACAAACCATCATACATATACAAAATTATAATATAAACTAAACAACAAAAAAAAACTTTACCATAACAACCTATAAAAAAATAATTACACATAATACCCCAAATA 9-I9I99III9IIIIIIII9I-I999I9II9II9I-II9IIIIIIIII9I-IIIII9III9II9999IIII9II-I9III-II--IIII--9IIII9IIIIII9I9II9I9-IIIII-IIIIIIIIIIIII AS:i:-56 XS:i:-48 XN:i:0 XM:i:8 XO:i:1 XG:i:1 NM:i:9 MD:Z:23T25T3C27A7T16C11T8T2 YS:i:-26 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:1639:1014_2:N:0:CTGTTAAC+ACCTCAGT/2 163 NW_026963318.1_GA_converted 2256429 1 126M1I4M = 2256571 272 ATTCAAAATATTAAAATTTCAACAAACTTATTATATTAAAAATAAAATTTTTTACCACAAAAAACCACATCACAAAAAAATACTCTAAATTTACTAAATTACAAAAAAATAAATCACACTTCATACACCCA I-IIIIIIIIIIIIIIIII9III9IIIIIIII9IIII-IIIIIIIIIIIII9IIIIIIIII9I99IIIIIIIIIIII--II9IIIIII9III9III9IIIIIII9IIII9IIIIIIIIII9IIIIIIIIII AS:i:-26 XS:i:-32 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:22A34T27A44 YS:i:-56 YT:Z:CP >>> Writing bisulfite mapping results to 270M_pe.bam <<< Reading in the sequence files ../data/270M_R1.fastp-trim.fq.gz and ../data/270M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1114:10241:28904_1:N:0:CTGTTGAC+ACCTCAGT NW_026963693.1 21905 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1117:46616:25219_1:N:0:CTGTTGAC+ACCTCAGT NW_026963379.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1120:18220:15960_1:N:0:CTGTTGAC+ACCTCAGT NW_026963781.1 28310 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1121:2254:14658_1:N:0:CTGTTGAC+ACCTCAGT NW_026963736.1 25932 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1125:7199:21675_1:N:0:CTGTTGAC+ACCTCAGT NW_026963794.1 13154 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:37714:3788_1:N:0:CTGTTGAC+ACCTCAGT NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:37731:3788_1:N:0:CTGTTGAC+ACCTCAGT NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1128:3646:21213_1:N:0:CTGTTGAC+ACCTCAGT NW_026963569.1 27453 Processed 3000000 sequence pairs so far Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1156:31807:7850_1:N:0:CTGTTGAC+ACCTCAGT NW_026963308.1 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1158:48704:5553_1:N:0:ATGTTGAC+ACCTCAGT NW_026963299.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1166:42570:29394_1:N:0:CTGTTGAC+ACCTCAGT NW_026963351.1 17507 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1185:3743:8662_1:N:0:CTGTTGAC+ACCTCAGT NW_026963347.1 1227508 Processed 8000000 sequence pairs so far Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1222:29031:3605_1:N:0:CTGTTGAC+ACCTCAGT NW_026963699.1 1 Processed 11000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1230:37674:22712_1:N:0:CTGTTGAC+ACCTCAGT NW_026963377.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1232:30763:5006_1:N:0:CTGTTGAC+ACCTCAGT NW_026963673.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1232:30796:5006_1:N:0:CTGTTGAC+ACCTCAGT NW_026963673.1 2 Processed 12000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1240:48064:1336_1:N:0:CTGTTGAC+ACCTCAGT NW_026963448.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1244:27688:10189_1:N:0:CTGTTGAC+ACCTCAGT NW_026963570.1 26076 Processed 13000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1250:37836:24589_1:N:0:CTGTTGAC+ACCTCAGT NW_026963377.1 2 Processed 14000000 sequence pairs so far Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1272:10816:10847_1:N:0:CTGTTGAC+ACCTCAGT NW_026963354.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1273:33442:25892_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 2 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1314:24573:1742_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 1 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1329:4658:1336_1:N:0:CTGTTGAC+ACCTCAGT NW_026963568.1 2 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1332:13025:25289_1:N:0:CTGTTGAC+ACCTCAGT NW_026963596.1 19314 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1341:24330:3760_1:N:0:CTGTTGAC+ACCTCAGT NW_026963743.1 1 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1367:14247:29170_1:N:0:CTGTTGAC+ACCTCAGT NC_007687.1 18536 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1404:45758:2135_1:N:0:CTGTTGAC+ACCTCAGT NW_026963568.1 2 Processed 26000000 sequence pairs so far Processed 27000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1418:7296:19406_1:N:0:CTGTTGAC+ACCTCAGT NW_026963372.1 501117 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1419:13470:7766_1:N:0:CTGTTGAC+ACCTCAGT NW_026963743.1 1 Processed 28000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1434:30181:3661_1:N:0:CTGTTGAC+ACCTCAGT NW_026963769.1 1 Processed 29000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1439:19596:23777_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1441:34648:12346_1:N:0:CTGTTGAC+ACCTCAGT NW_026963307.1 124884 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1448:27745:27629_1:N:0:CTGTTGAC+ACCTCAGT NW_026963772.1 1 Processed 30000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1451:32738:24197_1:N:0:CTGTTGAC+ACCTCAGT NW_026963704.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1453:32276:3199_1:N:0:CTGTTGAC+ACCTCAGT NW_026963394.1 27850 Processed 31000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1462:36930:22040_1:N:0:CTGTTGAC+ACCTCAGT NW_026963418.1 81291 Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Processed 34000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2103:40409:12767_1:N:0:CTGTTGAC+ACCTCAGT NW_026963568.1 2 Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2129:51123:12879_1:N:0:CTGTTGAC+ACCTCAGT NW_026963308.1 1 Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2145:23059:1252_1:N:0:CTGTTGAC+ACCTCAGT NW_026963772.1 22181 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2150:47482:25261_1:N:0:CTGTTGAC+ACCTCAGT NW_026963738.1 23719 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2173:14635:5945_1:N:0:CTGTTGAC+ACCTCAGT NW_026963772.1 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 LH00469:254:22HGFVLT4:2:2213:44229:15120_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2218:13931:18538_1:N:0:CTGTTGAC+ACCTCAGT NW_026963418.1 81291 Processed 44000000 sequence pairs so far Processed 45000000 sequence pairs so far Processed 46000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2251:32827:4740_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 1 Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2272:16149:20219_1:N:0:CTGTTGAC+ACCTCAGT NW_026963347.1 1227481 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2275:48210:6631_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 2 Processed 49000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2290:24977:9195_1:N:0:CTGTTGAC+ACCTCAGT NW_026963501.1 19440 Processed 50000000 sequence pairs so far Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2310:44124:22866_1:N:0:CTGTTGAC+ACCTCAGT NW_026963568.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2313:3144:3171_1:N:0:CTGTTGAC+ACCTCAGT NW_026963741.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2318:50719:15932_1:N:0:CTGTTGAC+ACCTCAGT NW_026963631.1 26251 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2343:29193:26662_1:N:0:CTGTTGAC+ACCTCAGT NW_026963500.1 55215 Processed 54000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2349:32544:20135_1:N:0:CTGTTGAC+ACCTCAGT NW_026963794.1 13152 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2357:32034:6477_1:N:0:CTGTTGAC+ACCTCAGT NW_026963369.1 120972 Processed 55000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2362:8550:3704_1:N:0:CTGTTGAC+ACCTCAGT NW_026963348.1 1 Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2380:46624:16773_1:N:0:CTGTTGAC+ACCTCAGT NW_026963377.1 2 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2392:39373:10721_1:N:0:CTGTTGAC+ACCTCAGT NW_026963443.1 1 Processed 58000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2405:21490:11758_1:N:0:CTGTTGAC+ACCTCAGT NW_026963427.1 1 Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2427:7360:28960_1:N:0:CTGTTGAC+ACCTCAGT NW_026963480.1 22701 Processed 61000000 sequence pairs so far Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2457:45394:6631_1:N:0:CTGTTGAC+ACCTCAGT NW_026963684.1 18466 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2458:5677:18958_1:N:0:CTGTTGAC+ACCTCAGT NW_026963791.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2461:13413:25654_1:N:0:CTGTTGAC+ACCTCAGT NW_026963470.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2463:46268:13691_1:N:0:CTGTTGAC+ACCTCAGT NW_026963741.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2463:46276:13705_1:N:0:CTGTTGAC+ACCTCAGT NW_026963741.1 1 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2485:32301:16437_1:N:0:CTGTTGAC+ACCTCAGT NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2488:25981:12725_1:N:0:CTGTTGAC+ACCTCAGT NW_026963743.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2489:27632:5300_1:N:0:CTGTTGAC+ACCTCAGT NW_026963802.1 2 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1260:25528:25976_1:N:0:CTGTTGAC+ACCTCAGT NC_086385.1 63222876 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1318:11827:17361_1:N:0:CTGTTGAC+ACCTCAGT NW_026963667.1 28287 Processed 71000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1320:14126:3521_1:N:0:CTGTTGAC+ACCTCAGT NW_026963595.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1346:30561:6449_1:N:0:CTGTTGAC+ACCTCAGT NW_026963743.1 1 Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1403:50630:4684_1:N:0:CTGTTGAC+ACCTCAGT NW_026963564.1 19030 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1415:49804:3872_1:N:0:CTGTTGAC+ACCTCAGT NW_026963705.1 2 Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1450:1672:23426_1:N:0:CTGTTGAC+ACCTCAGT NW_026963730.1 1 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1487:24637:11996_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 1 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2284:35554:26802_1:N:0:CTGTTGAC+ACCTCAGT NC_007687.1 18558 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2345:3784:1700_1:N:0:CTGTTGAC+ACCTCAGT NW_026963378.1 1 Processed 81000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2351:1664:8508_1:N:0:CTGTTGAC+ACCTCAGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2359:25333:9811_1:N:0:CTGTTGAC+ACCTCAGT NW_026963754.1 22936 Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2390:46462:2905_1:N:0:CTGTTGAC+ACCTCAGT NW_026963570.1 26078 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2416:34041:12725_1:N:0:CTGTTGAC+ACCTCAGT NW_026963480.1 22716 Processed 83000000 sequence pairs so far Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2475:1251:18075_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2496:25689:11212_1:N:0:CTGTTGAC+ACCTCAGT NW_026963725.1 2 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1278:50533:11828_1:N:0:CTGTTGAC+ACCTCAGT NW_026963299.1 2 Processed 89000000 sequence pairs so far Processed 90000000 sequence pairs so far Processed 91000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1432:43347:20541_1:N:0:CTGTTGAC+ACCTCAGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1432:43363:20541_1:N:0:CTGTTGAC+ACCTCAGT NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1447:39301:16983_1:N:0:CTGTTGAC+ACCTCAGT NW_026963806.1 1 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1449:42683:27293_1:N:0:CTGTTGAC+ACCTCAGT NW_026963740.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1463:31119:15456_1:N:0:CTGTTCAC+ACCTCAGT NW_026963720.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1463:31135:15456_1:N:0:CTGTTGAC+ACCTCAGT NW_026963720.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:1463:31127:15470_1:N:0:CTGTTGAC+ACCTCAGT NW_026963720.1 2 Processed 92000000 sequence pairs so far Processed 93000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2187:11123:7682_1:N:0:CTGTTGAC+ACCTCAGT NW_026963347.1 1227492 Processed 94000000 sequence pairs so far Processed 95000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2270:35942:6519_1:N:0:CTGTTGAC+ACCTCAGT NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2304:44989:13215_1:N:0:CTGTTGAC+ACCTCAGT NW_026963401.1 1 Processed 96000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2366:50840:21353_1:N:0:CTGTTGAC+ACCTCAGT NW_026963461.1 2 Processed 97000000 sequence pairs so far Processed 98000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00160:357:22J27KLT4:6:2456:12086:24981_1:N:0:CTGTTGAC+ACCTCAGT NW_026963705.1 2 Processed 99000000 sequence pairs so far 99002878 reads; of these: 99002878 (100.00%) were paired; of these: 41054588 (41.47%) aligned concordantly 0 times 18833203 (19.02%) aligned concordantly exactly 1 time 39115087 (39.51%) aligned concordantly >1 times 58.53% overall alignment rate 99002878 reads; of these: 99002878 (100.00%) were paired; of these: 41053381 (41.47%) aligned concordantly 0 times 18821843 (19.01%) aligned concordantly exactly 1 time 39127654 (39.52%) aligned concordantly >1 times 58.53% overall alignment rate Processed 99002878 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 396011512. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 396011512. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 396011512. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 396011512. Successfully deleted the temporary files 270M_R1.fastp-trim.fq.gz_C_to_T.fastq and 270M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 99002878 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2376841573 Total methylated C's in CpG context: 30048003 Total methylated C's in CHG context: 3698139 Total methylated C's in CHH context: 17272223 Total methylated C's in Unknown context: 448948 Total unmethylated C's in CpG context: 251244215 Total unmethylated C's in CHG context: 377936432 Total unmethylated C's in CHH context: 1696642561 Total unmethylated C's in Unknown context: 13304341 C methylated in CpG context: 10.7% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 6h 48m 29s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe