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. 10000000 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_se_bismark/subset_10000000'): /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_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/20190222_cgigas_se_bismark/subset_10000000 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 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 10000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file cgig_bsseq_all_R1.fastq.gz to cgig_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file cgig_bsseq_all_R1.fastq.gz (10000001 sequences in total) Input file is cgig_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/C_gigas/genomes/ 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 cgig_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/C_gigas/genomes/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1599:2153_1:N:0:TAGCTT 4 * 0 0 * * 0 0 TNGGGGTAGGTTGAATTTGTATTTTTTATGTAGTTTTTTGAGAAAGATTGA C#1AD;2@;D>> Writing bisulfite mapping results to cgig_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1773:34563_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3577:18659_1:N:0:TAGCTT C23010 2001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12835:3587_1:N:0:TAGCTT C23010 2002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:10421:24530_1:N:0:TAGCTT scaffold38030 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18665:62350_1:N:0:TAGCTT C34600 19430 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2988:100874_1:N:0:TAGCTT scaffold811 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:13327:43238_1:N:0:TAGCTT C28016 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:12755:63320_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:20213:64837_1:N:0:TAGCTT scaffold845 3217 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12588:36512_1:N:0:TAGCTT scaffold838 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:15893:2479_1:N:0:TAGCTT C35992 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10332:16567_1:N:0:TAGCTT C15208 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:19128:57495_1:N:0:TAGCTT C14656 214 Processed 1000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:6194:34264_1:N:0:TAGCTT scaffold38856 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:1976:74862_1:N:0:TAGCTT C15654 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:17016:83695_1:N:0:TAGCTT C15162 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1110:8021:96188_1:N:0:TAGCTT scaffold1895 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:7845:68788_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:20543:93295_1:N:0:TAGCTT scaffold38030 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1111:5799:96032_1:N:0:TAGCTT scaffold26586 3991 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:5325:37641_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:3805:88811_1:N:0:TAGCTT C33332 13914 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1112:7692:91397_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:18516:50545_1:N:0:TAGCTT C23010 2002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:21097:60128_1:N:0:TAGCTT scaffold39464 72101 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1114:21061:89547_1:N:0:TAGCTT scaffold42790 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:9662:19845_1:N:0:TAGCTT C14724 214 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:14174:28027_1:N:0:TAGCTT scaffold681 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:9463:37538_1:N:0:TAGCTT scaffold25910 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:10253:44431_1:N:0:TAGCTT scaffold33902 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1115:8202:63048_1:N:0:TAGCTT scaffold33742 2 Processed 2000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1116:1971:28732_1:N:0:TAGCTT C20886 1174 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1201:11745:34366_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1202:4837:35030_1:N:0:TAGCTT C32222 11025 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1202:4675:50032_1:N:0:TAGCTT C34418 18492 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1202:20402:88707_1:N:0:TAGCTT scaffold1359 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1203:12182:58735_1:N:0:TAGCTT scaffold33876 15779 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1203:10076:68867_1:N:0:TAGCTT scaffold221 207838 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1203:19553:84916_1:N:0:TAGCTT C31482 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1203:7598:91082_1:N:0:TAGCTT C22634 1872 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1204:7258:18231_1:N:0:TAGCTT scaffold36492 35558 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1204:4692:30668_1:N:0:TAGCTT scaffold998 153228 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1204:10882:82970_1:N:0:TAGCTT C22904 1957 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1205:2960:31454_1:N:0:TAGCTT C21854 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1205:9982:65799_1:N:0:TAGCTT C16622 349 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1206:11090:25238_1:N:0:TAGCTT C26688 4076 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1206:14430:79019_1:N:0:TAGCTT C23010 2001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1206:1401:88696_1:N:0:TAGCTT C28852 5906 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1207:9715:8062_1:N:0:TAGCTT C30430 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1207:1404:75751_1:N:0:TAGCTT C34600 19430 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1207:8439:81929_1:N:0:TAGCTT scaffold41902 137599 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1207:8338:84034_1:N:0:TAGCTT scaffold67 2 Processed 3000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1208:5613:74086_1:N:0:TAGCTT C23010 2001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1208:12652:82092_1:N:0:TAGCTT C14162 189 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1208:6354:90848_1:N:0:TAGCTT scaffold24070 2508 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1209:2381:44199_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1209:12796:61059_1:N:0:TAGCTT C15646 266 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1209:1757:76485_1:N:0:TAGCTT C21542 1416 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1209:2728:92564_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1210:7762:19095_1:N:0:TAGCTT scaffold38366 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1210:1459:21708_1:N:0:TAGCTT C17474 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1210:12973:39899_1:N:0:TAGCTT C14468 210 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1210:13942:42914_1:N:0:TAGCTT scaffold650 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1211:14032:18993_1:N:0:TAGCTT C13236 163 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1211:14913:22666_1:N:0:TAGCTT C16206 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1211:6654:67843_1:N:0:TAGCTT scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1211:16110:91525_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1211:11850:100859_1:N:0:TAGCTT C28430 5506 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1212:16290:18282_1:N:0:TAGCTT scaffold620 3381 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1212:15139:34329_1:N:0:TAGCTT scaffold38856 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1212:1416:41915_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1212:10030:58854_1:N:0:TAGCTT C21854 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1212:9970:86696_1:N:0:TAGCTT C13136 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1214:15798:11407_1:N:0:TAGCTT scaffold52 3659 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1214:3048:75820_1:N:0:TAGCTT C14656 214 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1215:10174:11135_1:N:0:TAGCTT scaffold1866 525892 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1215:6071:11763_1:N:0:TAGCTT C25616 1 Processed 4000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1215:11760:44570_1:N:0:TAGCTT C29764 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1215:19336:76957_1:N:0:TAGCTT C24604 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1301:19957:51952_1:N:0:TAGCTT scaffold806 114376 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1302:17969:67899_1:N:0:TAGCTT scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1303:1389:25589_1:N:0:TAGCTT C23732 2353 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1303:14402:73643_1:N:0:TAGCTT C23648 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1303:17477:95517_1:N:0:TAGCTT scaffold39244 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1304:16972:15425_1:N:0:TAGCTT C26492 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1304:1698:31473_1:N:0:TAGCTT C14220 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1304:2158:66186_1:N:0:TAGCTT C32222 11024 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1306:14437:21907_1:N:0:TAGCTT scaffold42790 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1306:20243:23399_1:N:0:TAGCTT scaffold33876 15778 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1306:1150:83570_1:N:0:TAGCTT C20294 983 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1307:15853:25438_1:N:0:TAGCTT scaffold428 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1307:13759:27470_1:N:0:TAGCTT scaffold38136 2 Processed 5000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1308:16237:51155_1:N:0:TAGCTT scaffold228 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1308:4728:66627_1:N:0:TAGCTT C32222 11024 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1308:13672:75987_1:N:0:TAGCTT scaffold38510 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1309:4360:70056_1:N:0:TAGCTT C16854 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1309:2780:79562_1:N:0:TAGCTT scaffold413 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1310:21135:22429_1:N:0:TAGCTT scaffold186 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1310:10269:86803_1:N:0:TAGCTT C32222 11023 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1311:1944:8727_1:N:0:TAGCTT C29980 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1311:6733:31089_1:N:0:TAGCTT C26374 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1311:16332:43067_1:N:0:TAGCTT C16206 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1311:7065:87703_1:N:0:TAGCTT C26582 4002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1312:10371:59127_1:N:0:TAGCTT scaffold42366 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1313:12839:22472_1:N:0:TAGCTT C21164 1273 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1313:17005:47777_1:N:0:TAGCTT C17016 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1313:14038:90079_1:N:0:TAGCTT C25616 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1313:3082:94392_1:N:0:TAGCTT scaffold37286 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:13829:2118_1:N:0:TAGCTT C34418 18492 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:20041:30743_1:N:0:TAGCTT scaffold33742 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:6627:46799_1:N:0:TAGCTT C29050 6113 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:15399:50649_1:N:0:TAGCTT C17966 505 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:15275:60062_1:N:0:TAGCTT C30946 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1314:7244:67862_1:N:0:TAGCTT scaffold41684 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1315:19081:8955_1:N:0:TAGCTT C32222 11024 Processed 6000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1315:21152:60959_1:N:0:TAGCTT scaffold688 1129 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1315:4285:69093_1:N:0:TAGCTT C34158 17297 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1316:16776:20836_1:N:0:TAGCTT scaffold958 664 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1316:19177:64936_1:N:0:TAGCTT C29070 6130 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2102:7174:31046_1:N:0:TAGCTT scaffold38510 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2102:16922:31351_1:N:0:TAGCTT scaffold38856 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2103:19696:12202_1:N:0:TAGCTT C26960 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2104:4262:31451_1:N:0:TAGCTT C14966 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2104:6385:32018_1:N:0:TAGCTT scaffold137 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2105:9339:3736_1:N:0:TAGCTT scaffold39598 74200 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2105:6427:35842_1:N:0:TAGCTT scaffold1112 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2105:6814:79900_1:N:0:TAGCTT C17512 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2105:10435:97570_1:N:0:TAGCTT scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2106:4517:7895_1:N:0:TAGCTT scaffold510 367292 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2106:9565:67624_1:N:0:TAGCTT scaffold715 156526 Processed 7000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2107:4339:4298_1:N:0:TAGCTT C22904 1961 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2107:18906:5512_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2107:9575:73566_1:N:0:TAGATT C15208 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2108:8488:9536_1:N:0:TAGCTT C18300 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2108:20110:24747_1:N:0:TAGCTT C24850 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2108:13740:28525_1:N:0:TAGCTT scaffold35660 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2108:11215:30075_1:N:0:TAGCTT C15208 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2109:18812:3179_1:N:0:TAGCTT C30046 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2109:2394:12344_1:N:0:TAGCTT C32222 11024 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2109:9607:23141_1:N:0:TAGCTT scaffold228 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2110:5329:28407_1:N:0:TAGCTT C18686 605 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2110:15763:34472_1:N:0:TAGCTT C14952 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2110:9984:43683_1:N:0:TAGCTT scaffold1864 99925 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2110:1506:49123_1:N:0:TAGCTT C27816 4945 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2110:12990:66062_1:N:0:TAGCTT C26774 4130 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2111:5873:41363_1:N:0:TAGCTT C17044 396 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2111:4586:44488_1:N:0:TAGCTT C23258 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2111:5813:44550_1:N:0:TAGCTT scaffold1184 23993 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2111:17314:58527_1:N:0:TAGCTT C28430 5506 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2111:11104:95676_1:N:0:TAGCTT scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2112:19145:11620_1:N:0:TAGCTT scaffold39732 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2112:16709:20694_1:N:0:TAGCTT scaffold249 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2112:18258:25713_1:N:0:TAGCTT scaffold33902 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2112:10155:57623_1:N:0:TAGCTT C16206 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2113:20295:23438_1:N:0:TAGCTT scaffold137 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2113:1661:29956_1:N:0:TAGCTT C32222 11024 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2113:18760:57319_1:N:0:TAGCTT C14952 2 Processed 8000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2114:11552:6658_1:N:0:TAGCTT C28430 5507 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2114:10291:20046_1:N:0:TAGCTA scaffold221 207836 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2114:18380:84805_1:N:0:TAGCTT C23968 2458 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2114:21276:93416_1:N:0:TAGCTT scaffold1028 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:1949:25963_1:N:0:TAGCTT scaffold702 10899 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:4194:39294_1:N:0:TAGCTT scaffold36736 37501 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:9576:40034_1:N:0:TAGCTT C15646 267 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:21157:41145_1:N:0:TAGCTT scaffold37154 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:19128:42819_1:N:0:TAGCTT scaffold31382 9227 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2115:3359:61771_1:N:0:TAGCTT scaffold387 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2116:12528:4474_1:N:0:TAGCTT scaffold775 145389 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2201:4958:2575_1:N:0:TAGCTT scaffold41550 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2201:13764:45842_1:N:0:TAGCTT C15208 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2203:20053:89664_1:N:0:TAGCTT scaffold1867 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2206:7546:23658_1:N:0:TAGCTT C30946 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2206:2769:31019_1:N:0:TACCTT scaffold38700 59861 Processed 9000000 sequences so far Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2207:4329:84353_1:N:0:TAGCTT scaffold1100 230270 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2207:3586:85724_1:N:0:TAGCTT scaffold23524 2188 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2208:8885:26534_1:N:0:TAGCTT C23732 2353 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2209:2892:50015_1:N:0:TAGCTT scaffold1397 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2209:5102:62090_1:N:0:TAGCTT C30166 7452 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2209:13278:72246_1:N:0:TAGCTT C23010 2001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2209:12758:98808_1:N:0:TAGCTT scaffold1864 99925 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2210:7662:33931_1:N:0:TAGCTT scaffold39884 79267 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2210:14059:71160_1:N:0:TAGCTT scaffold1100 230270 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2211:6094:58366_1:N:0:TAGCTT C32838 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2214:1136:13343_1:N:0:TAGCTT scaffold814 203813 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2214:7144:34064_1:N:0:TAGCTT scaffold1460 93623 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2301:9500:46869_1:N:0:TAGCTT C32222 11024 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2302:17199:30248_1:N:0:TAGCTT scaffold33742 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2302:4937:67280_1:N:0:TAGCTT C18686 605 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2303:4200:55528_1:N:0:TAGCTT C15208 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2303:7938:69226_1:N:0:TAGCTT scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2303:8470:95707_1:N:0:TAGCTT C22114 1667 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2304:15118:37791_1:N:0:TAGCTT C25882 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2304:6287:69293_1:N:0:TAGCTT scaffold36674 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2304:9655:92654_1:N:0:TAGCTT C23010 2003 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2305:3051:23757_1:N:0:TAGCTT scaffold34000 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2305:20735:50025_1:N:0:TAGCTA scaffold24958 2956 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:2306:18259:18739_1:N:0:TAGCTT C28430 5506 10000000 reads; of these: 10000000 (100.00%) were unpaired; of these: 4607676 (46.08%) aligned 0 times 2512667 (25.13%) aligned exactly 1 time 2879657 (28.80%) aligned >1 times 53.92% overall alignment rate 10000000 reads; of these: 10000000 (100.00%) were unpaired; of these: 4612068 (46.12%) aligned 0 times 2511580 (25.12%) aligned exactly 1 time 2876352 (28.76%) aligned >1 times 53.88% overall alignment rate Processed 10000000 sequences so far Successfully deleted the temporary file cgig_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 10000000 Number of alignments with a unique best hit from the different alignments: 5420968 Mapping efficiency: 54.2% Final Cytosine Methylation Report ================================= Total number of C's analysed: 45741783 Total methylated C's in CpG context: 1824351 Total methylated C's in CHG context: 287956 Total methylated C's in CHH context: 552527 Total methylated C's in Unknown context: 8793 Total unmethylated C's in CpG context: 5169991 Total unmethylated C's in CHG context: 9428745 Total unmethylated C's in CHH context: 28478213 Total unmethylated C's in Unknown context: 75064 C methylated in CpG context: 26.1% C methylated in CHG context: 3.0% C methylated in CHH context: 1.9% C methylated in Unknown context (CN or CHN): 10.5% Bismark completed in 0d 0h 49m 53s ==================== Bismark run complete ====================