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/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ (absolute path is '/gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/)' Processing sequences up to read no. 100000 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_pgenerosa_rrbs_se_bismark/subset_Pgenerosa_v070_100000'): /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_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_pgenerosa_rrbs_se_bismark/subset_Pgenerosa_v070_100000 Now reading in and storing sequence information of the genome specified in: /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ 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. 100000 from /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file pgen_bsseq_all_R1.fastq.gz to pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file pgen_bsseq_all_R1.fastq.gz (100001 sequences in total) Input file is pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ 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 pgen_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/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG 4 * 0 0 * * 0 0 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to pgen_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6416:3671_1:N:0:ATCACG PGA_scaffold65532__1_contigs__length_13710 13610 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3206:3918_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3973:3828_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4047:4144_1:N:0:ATCACG PGA_scaffold45488__1_contigs__length_1333 1237 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9092:4062_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20681:4212_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19035:4315_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14831:4639_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1348:4824_1:N:0:ATCACG PGA_scaffold805__1_contigs__length_19754 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7675:6371_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989293 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19232:6308_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10646:7090_1:N:0:ATCACG PGA_scaffold42185__1_contigs__length_1105 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3873:7275_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6313:7965_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13845:8879_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15388:9040_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12292:9405_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11678:9524_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6448:9781_1:N:0:ATCACG PGA_scaffold19151__1_contigs__length_2082 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15972:9803_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13692:10097_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3195:10952_1:N:0:ATCACG PGA_scaffold58363__1_contigs__length_1412 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13122:11093_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989297 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3974:11478_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10980:11552_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11522:11632_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4623:12077_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6489:12163_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7474:12098_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3330:12497_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989297 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9575:12310_1:N:0:ATCACG PGA_scaffold21709__1_contigs__length_3695 3594 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19857:13678_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16275:14515_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1085 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2129:15188_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7236:15233_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6904:15435_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20447:15349_1:N:0:ATCACG PGA_scaffold9226__1_contigs__length_1034 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8365:15800_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12413:15822_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14907:16248_1:N:0:ATCACG PGA_scaffold56753__1_contigs__length_3010 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15434:16045_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5458:17408_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1516:17681_1:N:0:ATCACG PGA_scaffold30867__1_contigs__length_1516 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20239:17664_1:N:0:ATCACG PGA_scaffold52208__1_contigs__length_6200 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6312:18088_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6219:18857_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12907:19243_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18316:19453_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5161:19644_1:N:0:ATCACG PGA_scaffold71558__1_contigs__length_10954 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1407:20205_1:N:0:ATCACG PGA_scaffold68393__1_contigs__length_1425 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9301:20416_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7001:20835_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5607:21220_1:N:0:ATCACG PGA_scaffold68634__1_contigs__length_8528 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4699:21694_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8101:21533_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4658:22456_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1678:23029_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6493:23041_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10912:23740_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989297 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18939:23977_1:N:0:ATCACG PGA_scaffold21709__1_contigs__length_3695 3594 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3544:24190_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16206:24362_1:N:0:ATCACG PGA_scaffold63966__1_contigs__length_6244 6144 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1652:24932_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15667:24962_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989293 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20145:24945_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18062:25125_1:N:0:ATCACG PGA_scaffold46179__1_contigs__length_1326 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10797:25376_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20748:25294_1:N:0:ATCACG PGA_scaffold52448__1_contigs__length_6871 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14270:26632_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3323:26853_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8904:26863_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989293 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11864:26806_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16067:26968_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8655:27251_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3640:27718_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12987:27564_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18374:27963_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989292 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20578:28801_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10338:29902_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4053:30305_1:N:0:ATCACG PGA_scaffold34601__1_contigs__length_1043 960 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13490:30813_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19571:31179_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13110:31372_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989297 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17216:31410_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3159:31974_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13729:32029_1:N:0:ATCACG PGA_scaffold48161__1_contigs__length_1209 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5855:32292_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11207:32870_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989292 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8418:33090_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17204:33331_1:N:0:ATCATG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2511:34933_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989292 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10237:34966_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10665:34864_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8382:35065_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3135:35429_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13399:35332_1:N:0:ATCACG PGA_scaffold7695__1_contigs__length_2232 2135 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17569:35412_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989295 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3882:36460_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5437:36841_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14829:36769_1:N:0:ATCACG PGA_scaffold48911__1_contigs__length_1808 1707 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14324:37124_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2379:37279_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2101:37716_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19473:38568_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11838:38805_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1090 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6010:39641_1:N:0:ATCACG PGA_scaffold34601__1_contigs__length_1043 959 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20666:39512_1:N:0:ATCACG PGA_scaffold34601__1_contigs__length_1043 960 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15933:40607_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10610:41002_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798925 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14367:42405_1:N:0:ATCACG PGA_scaffold64880__1_contigs__length_1934 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15508:43151_1:N:0:ATCACG PGA_scaffold12776__1_contigs__length_1086 985 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1419:44486_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14785:44495_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989303 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4210:44750_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4479:45035_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5548:45348_1:N:0:ATCACG PGA_scaffold33753__1_contigs__length_1972 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10147:45294_1:N:0:ATCACG PGA_scaffold842__1_contigs__length_6824 6744 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4363:46076_1:N:0:ATCACG PGA_scaffold55977__1_contigs__length_5671 5570 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9205:46157_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989297 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19901:46259_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4011:46712_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989293 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2340:46814_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6878:47214_1:N:0:ATCACG PGA_scaffold19818__1_contigs__length_1159 1059 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16301:47371_1:N:0:ATCACG PGA_scaffold32302__1_contigs__length_3672 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9295:47828_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1088 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16038:48486_1:N:0:ATCACG PGA_scaffold17225__1_contigs__length_1255 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18012:48374_1:N:0:ATCACG PGA_scaffold71790__1_contigs__length_1978 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:21106:48323_1:N:0:ATCACG PGA_scaffold47144__1_contigs__length_1542 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1769:48854_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4514:48762_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989294 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8461:48977_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10948:48763_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 38961 (38.96%) aligned 0 times 21612 (21.61%) aligned exactly 1 time 39427 (39.43%) aligned >1 times 61.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were unpaired; of these: 39290 (39.29%) aligned 0 times 21479 (21.48%) aligned exactly 1 time 39231 (39.23%) aligned >1 times 60.71% overall alignment rate Successfully deleted the temporary file pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 100000 Number of alignments with a unique best hit from the different alignments: 56329 Mapping efficiency: 56.3% Final Cytosine Methylation Report ================================= Total number of C's analysed: 909434 Total methylated C's in CpG context: 28849 Total methylated C's in CHG context: 4725 Total methylated C's in CHH context: 8067 Total methylated C's in Unknown context: 205 Total unmethylated C's in CpG context: 105432 Total unmethylated C's in CHG context: 187465 Total unmethylated C's in CHH context: 574896 Total unmethylated C's in Unknown context: 2073 C methylated in CpG context: 21.5% C methylated in CHG context: 2.5% C methylated in CHH context: 1.4% C methylated in Unknown context (CN or CHN): 9.0% Bismark completed in 0d 0h 1m 31s ==================== Bismark run complete ====================