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/C_gigas/genomes/ (absolute path is '/gscratch/srlab/sam/data/C_gigas/genomes/)' Processing sequences up to read no. 5000000 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/20190222_cgigas_pe_bismark/subset_5000000'): /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.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/20190222_cgigas_pe_bismark/subset_5000000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_gigas/genomes/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 5000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz Writing a C -> T converted version of the input file cgig_bsseq_pe_all_R1.fastq.gz to cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file cgig_bsseq_pe_all_R1.fastq.gz (5000001 sequences in total) Processing reads up to sequence no. 5000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Writing a G -> A converted version of the input file cgig_bsseq_pe_all_R2.fastq.gz to cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file cgig_bsseq_pe_all_R2.fastq.gz (5000001 sequences in total) Input files are cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_gigas/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1 99 scaffold750_CT_converted 577176 1 36M = 577200 60 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG CC@FDFFFHHGHHJFBGIIJJIJEHGIJIJJJJJJG AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2 147 scaffold750_CT_converted 577200 1 36M = 577176 -60 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAG GJJJIJJJJJJJJJJJJJJJJJJHHHHHD;FFFCC@ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1 83 scaffold393_GA_converted 143720 1 36M = 143706 -50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT GJJJJJJIJIGHEJIJJIIGBFJHHGHHFFFDF@CC AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2 163 scaffold393_GA_converted 143706 1 36M = 143720 50 CTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCT @CCFFF;DHHHHHJJJJJJJJJJJJJJJJJJIJJJG AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to cgig_bsseq_pe_all_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1101:5142:25699 C24196 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1105:4856:63835 C22548 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1110:1457:54826 scaffold43686 300769 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1110:4272:93059 C21764 1511 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1116:2368:7379 scaffold38090 52535 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1202:5993:5262 scaffold32624 12059 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1311:4068:17280 scaffold31954 10506 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2110:7883:8526 scaffold820 12177 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2115:13896:21944 C29202 6296 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2115:14740:74866 scaffold968 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2210:10409:80281 C24562 2765 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2302:18111:87639 scaffold1543 75281 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2304:13025:52866 scaffold514 545590 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1108:3243:64899 C24850 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1116:18282:33267 scaffold422 571151 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1212:4119:92664 C22844 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1309:13364:61734 scaffold40002 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:13488:58831 C29914 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:1902:90967 C16312 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:12466:35880 C19632 793 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2202:13231:64191 C30946 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2211:17251:49236 C31982 10534 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2305:9793:51855 C13670 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2307:13437:94978 C16318 296 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:17999:76027 C22114 1649 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:2217:17764 scaffold37906 49307 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2316:8125:61582 scaffold43708 307072 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:15396:85261 C23682 2315 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:10564:43163 scaffold40526 93686 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1111:5051:9548 scaffold36778 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1202:10373:14932 C29882 7083 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1301:6790:53328 C15378 225 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:3458:12677 scaffold26300 3768 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:7978:77375 C26010 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1308:13296:94127 scaffold931 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:3710:37333 scaffold90 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:6452:93474 scaffold920 665 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:6635:92485 scaffold33428 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:16518:47570 scaffold34032 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2112:4733:11201 scaffold546 671116 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:3911:78328 C26198 3711 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:6375:73457 C19902 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:20853:68622 C28408 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2308:14277:82004 C19356 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2308:11707:84503 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2309:2663:87373 scaffold1220 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2313:18611:77086 scaffold34894 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:2615:18288 C27276 4482 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1102:4511:90431 C20550 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1104:13520:60250 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1105:4960:61551 C21312 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1105:18091:97546 C14780 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1106:17676:39873 C34436 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1108:18717:6257 C26570 3969 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1109:19378:41363 C23682 2306 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1109:5793:59367 C19406 748 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1110:11367:80644 scaffold352 319595 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:9395:30477 scaffold715 156505 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:1586:64754 scaffold24412 2614 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:14221:82192 scaffold641 4064 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1112:14836:100573 scaffold38360 55240 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1113:14347:96274 C26690 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1115:13495:13495 C33182 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1116:19232:72690 C13344 149 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1201:16527:86659 C28184 5253 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1202:15308:59676 scaffold36314 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:3534:33827 C32328 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:7944:66249 C31714 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:15395:77863 scaffold716 401243 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1208:12408:74143 C25056 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:15877:27476 scaffold38908 63646 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:10164:38200 C19984 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:7797:66314 scaffold514 545550 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:15884:69342 C15630 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:17417:13163 C32578 11932 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:4886:49407 scaffold40526 93683 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:13953:75261 C22800 1908 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1212:12431:25421 scaffold1085 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1216:3941:29249 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1216:16197:97521 scaffold38756 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1307:9592:12311 C28340 5399 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1308:15516:23525 C19252 711 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1313:7436:69713 scaffold221 207814 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1313:9714:77612 C21312 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:13724:42028 C27928 5014 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:2088:72584 scaffold30 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1316:2908:34542 C30766 8266 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1316:12069:89512 scaffold1001 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2104:15153:77817 scaffold1218 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2106:16911:53664 C21726 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2107:2485:75708 C23024 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2109:3985:63813 C26570 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2109:6989:91975 scaffold1223 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2110:9523:78213 scaffold251 122291 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2110:7379:99442 scaffold37 261120 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:9774:29909 C30946 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:12370:62819 C19354 739 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:5312:88326 scaffold34534 19391 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2113:10153:76819 C24320 2605 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2114:7979:89608 C23264 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:20981:59227 scaffold1354 417413 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:12738:93240 C20728 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2116:15974:9932 scaffold38274 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2116:8237:14099 C15086 212 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2206:7524:16301 scaffold18778 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2209:17741:92187 scaffold680 70132 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2209:2271:96455 scaffold36630 36587 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2212:20636:44893 scaffold44 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2214:7229:67817 C31714 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2215:15786:84949 C24524 2711 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2305:11956:23372 scaffold365 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:9970:70146 C34176 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:12585:97652 C30434 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2310:5439:93452 scaffold30010 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2311:2721:15005 scaffold1726 437309 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2311:1661:43781 C24640 2773 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:12959:12687 C33128 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:12075:38838 C17244 396 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:13884:60192 scaffold793 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2313:16822:44879 C13242 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2314:2279:54502 C29322 6403 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2314:10595:78018 C29006 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2315:14181:28888 scaffold1433 1255 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1101:8864:52220 scaffold32252 11030 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1101:8641:66384 C17922 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1102:9671:25782 C16402 311 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1102:19025:69843 C33666 14997 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:14071:17161 C29992 7209 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:19817:55984 C20856 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:14795:66871 C27712 4828 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:8619:15833 scaffold208 247942 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:7511:88472 C28070 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:6910:89443 scaffold41898 137745 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:13129:96402 scaffold1470 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:16685:12125 scaffold25284 3085 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:10387:20850 C34176 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:14877:28724 scaffold1868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:11436:28955 scaffold37990 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:18030:42317 scaffold344 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:7395:85920 scaffold451 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:2237:4464 C24814 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:2201:36372 scaffold40194 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:3828:75719 scaffold43084 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:16205:80479 C24232 2564 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:4096:23805 C32438 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:2461:27760 C13046 133 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:13386:31985 C24688 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:16315:52756 scaffold31320 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:20668:85116 C15156 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:12606:44182 scaffold38354 54689 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:11978:68572 C15352 230 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:3862:73789 scaffold24 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:17333:4147 scaffold39368 69005 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:8073:6385 scaffold1261 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:11368:41024 C32994 12988 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1110:1876:11962 scaffold36936 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1111:12589:78270 scaffold607 805 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:8795:13082 C19576 779 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:5862:22594 scaffold43608 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:9959:30021 C34634 19666 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:20362:86184 C19838 833 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:3425:94171 scaffold579 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:7425:2747 scaffold34956 21421 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:12122:48110 C24204 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:13931:48573 C30946 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:5981:51824 scaffold33066 13114 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:17357:54570 C24964 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:10628:67478 scaffold37558 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:16303:84513 C29992 7209 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:16957:94805 C32108 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:14368:98032 C34712 20063 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:18175:13608 scaffold1376 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:11752:24492 scaffold157 679231 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:1472:53479 scaffold33518 14456 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:18292:77959 scaffold451 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:2993:84648 scaffold31792 10145 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:4352:20180 C23490 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:7310:20878 scaffold41828 133120 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:12811:25674 C16738 337 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:16304:48154 scaffold39732 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:3592:61332 C25546 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:13457:78936 scaffold318 2186 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1201:4711:12749 C31572 1 5000000 reads; of these: 5000000 (100.00%) were paired; of these: 3310946 (66.22%) aligned concordantly 0 times 931299 (18.63%) aligned concordantly exactly 1 time 757755 (15.16%) aligned concordantly >1 times 33.78% overall alignment rate 5000000 reads; of these: 5000000 (100.00%) were paired; of these: 3321030 (66.42%) aligned concordantly 0 times 922480 (18.45%) aligned concordantly exactly 1 time 756490 (15.13%) aligned concordantly >1 times 33.58% overall alignment rate Processed 5000000 sequence pairs so far Processed 5000000 sequences in total Successfully deleted the temporary files cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 5000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 42833940 Total methylated C's in CpG context: 760506 Total methylated C's in CHG context: 20354 Total methylated C's in CHH context: 72398 Total methylated C's in Unknown context: 5702 Total unmethylated C's in CpG context: 4201008 Total unmethylated C's in CHG context: 6972501 Total unmethylated C's in CHH context: 30807173 Total unmethylated C's in Unknown context: 83877 C methylated in CpG context: 15.3% C methylated in CHG context: 0.3% C methylated in CHH context: 0.2% C methylated in unknown context (CN or CHN): 6.4% Bismark completed in 0d 0h 41m 17s ==================== Bismark run complete ====================