Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ (absolute path is '/gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/)' Processing sequences up to read no. 500000 from the input file 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 Input files to be analysed (in current folder '/gscratch/scrubbed/samwhite/outputs/20190224_olurida_se_bismark/subset_500000'): /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.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!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/samwhite/outputs/20190224_olurida_se_bismark/subset_500000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 500000 from /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file olur_bsseq_all_R1.fastq.gz to olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file olur_bsseq_all_R1.fastq.gz (500001 sequences in total) Input file is olur_bsseq_all_R1.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from olur_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 0 Contig68945_CT_converted 3260 40 51M * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15A35 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from olur_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 4 * 0 0 * * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI YT:Z:UU >>> Writing bisulfite mapping results to olur_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4347:2281_1:N:0:GGCTAC Contig150331 1132 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5376:3134_1:N:0:GGCTAC Contig91563 4015 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17166:4061_1:N:0:GGCTAC Contig137622 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5908:8127_1:N:0:GGCTAC Contig62700 12542 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:15584:10948_1:N:0:GGCTAC Contig136606 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20895:11557_1:N:0:GGCTAC Contig61059 13263 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:16834:12905_1:N:0:GGCTAC Contig103061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13764:15530_1:N:0:GGCTAC Contig58471 12756 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5252:17437_1:N:0:GGCTAC Contig64696 1930 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4688:18123_1:N:0:GGCTAC Contig58295 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:9031:21273_1:N:0:GGCTAC Contig81887 7685 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11541:23175_1:N:0:GGCTAC Contig31194 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4494:28672_1:N:0:GGCTAC Contig86549 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1455:32979_1:N:0:GGCTAC Contig89321 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13971:35149_1:N:0:GGCTAC Contig8342 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20218:35803_1:N:0:GGCTAC Contig4243 4822 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8283:36165_1:N:0:GGCTAC Contig91786 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:19453:43618_1:N:0:GGCTAC Contig73061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3706:48640_1:N:0:GGCTAC Contig61175 21107 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11593:48655_1:N:0:GGCTAC Contig7889 4048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:2939:50408_1:N:0:GGCTAC Contig85771 3766 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:6515:51728_1:N:0:GGCTAC Contig170236 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18033:53654_1:N:0:GGCTAC Contig155853 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4646:54966_1:N:0:GGCTAC Contig95638 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4910:55470_1:N:0:GGCTAC Contig273050 2048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18569:55548_1:N:0:GGCTAC Contig151615 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1532:60430_1:N:0:GGCTAC Contig198517 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3845:61407_1:N:0:GGCTAC Contig140986 5961 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18023:64092_1:N:0:GGCTAC Contig136884 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17964:68817_1:N:0:GGCTAC Contig147984 3646 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:7470:74674_1:N:0:GGCTAC Contig73164 4170 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13391:83918_1:N:0:GGCTAC Contig50092 14727 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:12498:85448_1:N:0:GGCTAC Contig77238 1311 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8953:94533_1:N:0:GGCTAC Contig68181 2475 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15772:4429_1:N:0:GGCTAC Contig97752 7990 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3321:4677_1:N:0:GGCTAC Contig114458 2272 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6273:7840_1:N:0:GGCTAC Contig123727 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:21017:7890_1:N:0:GGCTAC Contig33816 21218 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5176:8223_1:N:0:GGCTAC Contig556401 1014 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:12079:12646_1:N:0:GGCTAC Contig77554 4667 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:17607:14045_1:N:0:GGCTAC Contig81818 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:1819:17979_1:N:0:GGCTAC Contig114505 4631 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5847:20131_1:N:0:GGCTAC Contig149964 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:12424:23388_1:N:0:GGCTAC Contig46164 2603 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5841:25217_1:N:0:GGCTAC Contig127394 5030 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2570:25922_1:N:0:GGCTAC Contig24992 2193 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3167:35049_1:N:0:GGCTAC Contig111992 1806 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2648:36615_1:N:0:GGCTAC Contig121514 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:8099:37675_1:N:0:GGCTAC Contig194027 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6216:38455_1:N:0:GGCTAC Contig107186 1310 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:19081:38525_1:N:0:GGCTAC Contig134324 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:18954:38781_1:N:0:GGCTAC Contig109433 4007 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:13755:39923_1:N:0:GGCTAC Contig68297 3711 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:8788:41696_1:N:0:GGCTAC Contig62739 10345 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:11430:44806_1:N:0:GGCTAC Contig8535 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:14607:45785_1:N:0:GGCTAC Contig126469 3513 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6724:48048_1:N:0:GGCTAC Contig127062 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:14390:52873_1:N:0:GGCTAC Contig650 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:9078:53112_1:N:0:GGCTAC Contig46651 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:11107:53125_1:N:0:GGCTAC Contig198911 1122 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:16570:53767_1:N:0:GGCTAC Contig64786 25154 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:20708:54777_1:N:0:GGCTAC Contig101805 1365 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5643:55915_1:N:0:GGCTAC Contig96536 3416 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3997:61528_1:N:0:GGCTAC Contig91261 7142 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6382:62705_1:N:0:GGCTAC Contig74658 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:13854:66869_1:N:0:GGCTAC Contig211510 1143 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2343:72750_1:N:0:GGCTAC Contig16586 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10448:73575_1:N:0:GGCTAC Contig1091 23957 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6298:74422_1:N:0:GGCTAC Contig137459 985 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:9736:79930_1:N:0:GGCTAC Contig65230 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15928:80672_1:N:0:GGCTAC Contig1994 17848 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:20752:85792_1:N:0:GGCTAC Contig418836 1074 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10938:86965_1:N:0:GGCTAC Contig128222 1197 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10527:87362_1:N:0:GGCTAC Contig23361 1427 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:18067:94594_1:N:0:GGCTAC Contig120994 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2470:95310_1:N:0:GGCTAC Contig88172 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5618:95600_1:N:0:GGCTAC Contig189411 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10794:100257_1:N:0:GGCTAC Contig206446 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15573:101022_1:N:0:GGCTAC Contig345869 1166 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:6036:5254_1:N:0:GGCTAC Contig193606 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15817:6057_1:N:0:GGCTAC Contig30194 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12364:9882_1:N:0:GGCTAC Contig98011 3408 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:1678:18353_1:N:0:GGCTAC Contig65230 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17282:22648_1:N:0:GGCTAC Contig8057 8167 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:19746:22654_1:N:0:GGCTAC Contig111317 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17334:23314_1:N:0:GGCTAC Contig7028 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4673:25988_1:N:0:GGCTAC Contig213444 4112 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18367:26160_1:N:0:GGCTAC Contig110263 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:19007:27419_1:N:0:GGCTAC Contig90762 3368 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12801:30895_1:N:0:GGCTAC Contig16235 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5112:35398_1:N:0:GGCTAC Contig85061 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5890:36562_1:N:0:GGCTAC Contig67597 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4934:37574_1:N:0:GGCTAC Contig95763 1374 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14929:42044_1:N:0:GGCTAC Contig7930 3379 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:13418:42617_1:N:0:GGCTAC Contig49094 2904 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15033:43782_1:N:0:GGCTAC Contig32939 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15778:43874_1:N:0:GGCTAC Contig97652 5228 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15760:46002_1:N:0:GGCTAC Contig204217 7743 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18210:53520_1:N:0:GGCTAC Contig36106 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:11654:56663_1:N:0:GGCTAC Contig93947 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:1338:57142_1:N:0:GGCTAC Contig67 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:10331:57742_1:N:0:GGCTAC Contig64786 25155 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17827:58655_1:N:0:GGCTAC Contig72382 12231 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:11735:62087_1:N:0:GGCTAC Contig39678 4941 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:13004:65617_1:N:0:GGCTAC Contig62375 9700 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:9833:65975_1:N:0:GGCTAC Contig103734 1366 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14848:67897_1:N:0:GGCTAC Contig36582 4635 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12965:70136_1:N:0:GGCTAC Contig157976 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4308:73258_1:N:0:GGCTAC Contig50564 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:8499:74655_1:N:0:GGCTAC Contig413 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16836:75844_1:N:0:GGCTAC Contig86765 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18623:76961_1:N:0:GGCTAC Contig213835 1407 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16022:77894_1:N:0:GGCTAC Contig66428 6742 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:10286:78382_1:N:0:GGCTAC Contig2813 17268 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16386:79815_1:N:0:GGCTAC Contig38293 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15793:82499_1:N:0:GGCTAC Contig32939 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:6237:83094_1:N:0:GGCTAC Contig75451 2622 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:8553:84252_1:N:0:GGCTAC Contig38333 26945 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16694:86692_1:N:0:GGCTAC Contig147984 3647 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:21154:87123_1:N:0:GGCTAC Contig128854 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:2395:88314_1:N:0:GGCTAC Contig83012 3554 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5759:90844_1:N:0:GGCTAC Contig51466 10978 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:9745:91779_1:N:0:GGCTAC Contig118742 3820 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17758:92828_1:N:0:GGCTAC Contig70667 3887 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14299:93925_1:N:0:GGCTAC Contig57650 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4189:95750_1:N:0:GGCTAC Contig9137 6876 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12447:100451_1:N:0:GGCTAC Contig208557 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19544:4462_1:N:0:GGCTAC Contig179264 3782 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17823:5999_1:N:0:GGCTAC Contig151615 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:1699:7087_1:N:0:GGCTAC Contig93675 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14987:7899_1:N:0:GGCTAC Contig41004 31798 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2483:10322_1:N:0:GGCTAC Contig148895 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2901:16538_1:N:0:GGCTAC Contig171315 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14181:16977_1:N:0:GGCTAC Contig16086 20557 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8919:17339_1:N:0:GGCTAC Contig102373 1663 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2941:17665_1:N:0:GGCTAC Contig127398 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:16281:18385_1:N:0:GGCTAC Contig290 36246 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:4149:19352_1:N:0:GGCTAC Contig84697 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14371:25216_1:N:0:GGCTAC Contig17041 8271 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:15579:26480_1:N:0:GGCTAC Contig1349 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17031:29505_1:N:0:GGCTAC Contig110389 1664 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17720:29948_1:N:0:GGCTAC Contig206614 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:11833:30884_1:N:0:GGCTAC Contig52426 7827 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:10923:34077_1:N:0:GGCTAC Contig59187 1690 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8581:39185_1:N:0:GGCTAC Contig90228 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:6831:39343_1:N:0:GGCTAC Contig166943 2342 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9360:41827_1:N:0:GGCTAC Contig24480 2499 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18914:42070_1:N:0:GGCTAC Contig107422 1855 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18333:43149_1:N:0:GGCTAC Contig205100 10565 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:13885:58267_1:N:0:GGCTAC Contig196877 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9090:69308_1:N:0:GGCTAC Contig31255 10100 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:12952:70101_1:N:0:GGCTAC Contig131711 9645 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8168:72224_1:N:0:GGCTAC Contig118248 7930 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:7754:72865_1:N:0:GGCTAC Contig33842 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:12673:73821_1:N:0:GGCTAC Contig6585 5507 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19238:75099_1:N:0:GGCTAC Contig131517 3002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19604:79031_1:N:0:GGCTAC Contig89262 1263 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17542:80478_1:N:0:GGCTAC Contig6714 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2563:81240_1:N:0:GGCTAC Contig48296 10890 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:4160:88033_1:N:0:GGCTAC Contig20637 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:6657:88109_1:N:0:GGCTAC Contig95655 2322 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18923:89867_1:N:0:GGCTAC Contig86018 9276 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14698:92671_1:N:0:GGCTAC Contig23469 11586 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:7283:93433_1:N:0:GGCTAC Contig133242 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:13707:93649_1:N:0:GGCTAC Contig45942 12254 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9414:94760_1:N:0:GGCTAC Contig57641 5469 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:15313:98529_1:N:0:GGCTAC Contig188808 1269 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1348:2547_1:N:0:GGCTAC Contig9137 6876 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:2877:2590_1:N:0:GGCTAC Contig39302 12483 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:10137:4390_1:N:0:GGCTAC Contig57162 11486 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:6676:4738_1:N:0:GGCTAC Contig157738 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:17436:6235_1:N:0:GGCTAC Contig41280 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:12454:7373_1:N:0:GGCTAC Contig207431 1743 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:18377:10351_1:N:0:GGCTAC Contig109879 2095 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:7533:11575_1:N:0:GGCTAC Contig73872 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:20490:13736_1:N:0:GGCTAC Contig28227 54605 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:18759:16576_1:N:0:GGCTAC Contig8057 8167 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1652:21903_1:N:0:GGCTAC Contig112610 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:15386:25680_1:N:0:GGCTAC Contig65111 12336 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:2697:27461_1:N:0:GGCTAC Contig4832 2969 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:4285:27719_1:N:0:GGCTAC Contig117132 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5911:27817_1:N:0:GGCTAC Contig23140 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:13013:28459_1:N:0:GGCTAC Contig84887 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:19702:30587_1:N:0:GGCTAC Contig148373 6480 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5977:31466_1:N:0:GGCTAC Contig126469 3513 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8218:35433_1:N:0:GGCTAC Contig100414 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:16055:36626_1:N:0:GGCTAC Contig93047 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8325:43624_1:N:0:GGCTAC Contig35960 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:14875:44375_1:N:0:GGCTAC Contig173239 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8631:45772_1:N:0:AGCTAC Contig128293 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:17139:47046_1:N:0:GGCTAC Contig199767 7404 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:9669:52618_1:N:0:GGCTAT Contig32939 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:19149:61639_1:N:0:GGCTAC Contig123907 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1575:62781_1:N:0:GGCTAC Contig63594 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5292:65122_1:N:0:GGCTAC Contig203883 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1837:65724_1:N:0:GGCTAC Contig41141 1 500000 reads; of these: 500000 (100.00%) were unpaired; of these: 185356 (37.07%) aligned 0 times 102300 (20.46%) aligned exactly 1 time 212344 (42.47%) aligned >1 times 62.93% overall alignment rate 500000 reads; of these: 500000 (100.00%) were unpaired; of these: 185272 (37.05%) aligned 0 times 102902 (20.58%) aligned exactly 1 time 211826 (42.37%) aligned >1 times 62.95% overall alignment rate Successfully deleted the temporary file olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 500000 Number of alignments with a unique best hit from the different alignments: 271823 Mapping efficiency: 54.4% Final Cytosine Methylation Report ================================= Total number of C's analysed: 2390699 Total methylated C's in CpG context: 120842 Total methylated C's in CHG context: 13800 Total methylated C's in CHH context: 27331 Total methylated C's in Unknown context: 719 Total unmethylated C's in CpG context: 279413 Total unmethylated C's in CHG context: 486986 Total unmethylated C's in CHH context: 1462327 Total unmethylated C's in Unknown context: 8651 C methylated in CpG context: 30.2% C methylated in CHG context: 2.8% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 7.7% Bismark completed in 0d 0h 3m 0s ==================== Bismark run complete ====================