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_v073/ (absolute path is '/gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v073/)' 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/20190222_geo_rrbs_bismark/subset_Pgenerosa_v073_500000'): /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_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_geo_rrbs_bismark/subset_Pgenerosa_v073_500000 Now reading in and storing sequence information of the genome specified in: /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v073/ 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/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 500000 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 (500001 sequences in total) Processing reads up to sequence no. 500000 from /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Writing a G -> A converted version of the input file pgen_bsseq_all_R2.fastq.gz to pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file pgen_bsseq_all_R2.fastq.gz (500001 sequences in total) Input files are pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v073/ 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 pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_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: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 99 PGA_scaffold71710__1_contigs__length_40502_CT_converted 40348 40 50M = 40348 -50 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to pgen_bsseq_all_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14032:3053_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7726:3624_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 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:5:2301:10593:5178_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:4623:12077_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15228:13489_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9736:14242_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4542:15045_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20327:15253_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:7001:20835_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7539:21586_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 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:5:2301:18807:23475_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:1834:27730_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7779:27669_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:11200:31541_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:5855:32292_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4156:34487_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989315 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:5:2301:5437:36841_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14324:37124_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2101:37716_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18845:40323_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 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:5:2301:19579:43965_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 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:5:2301:4210:44750_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:5:2301:16746:47406_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3739:47602_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7807:48626_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18150:50026_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6342:50954_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10934:52441_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13220:53499_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798925 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3717:54626_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4829:54833_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19470:54849_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6417:55494_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5247:55639_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798935 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7173:56224_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5992:57751_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13118:57835_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6003:58706_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7868:61908_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19076:61837_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17300:62105_1:N:0:ATCACG PGA_scaffold46916__1_contigs__length_36995 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18114:63590_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19152:65486_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6165:67152_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5601:68656_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14980:73309_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13137:73623_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11902:76491_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19574:78139_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13183:79132_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9521:80297_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7413:82454_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6181:83001_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17878:84063_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6792:84317_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15488:85331_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19988:85583_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18795:85865_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16622:87956_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20298:88315_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2412:92702_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4214:92553_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14253:96218_1:N:0:ATCACG PGA_scaffold67687__1_contigs__length_62665 62568 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2174:100130_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12533:2329_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17169:7826_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:4843:10173_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5103:12122_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11394:13157_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9160:18281_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19748:18521_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14301:21559_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8852:22850_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10412:27913_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8620:28439_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16200:28469_1:N:0:GTCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11189:29532_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8932:29823_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6997:30389_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18760:34456_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1162:35308_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1870:42087_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14179:42955_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5604:43016_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12774:47792_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9531:48233_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:3833:50233_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1192:51827_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8286:55759_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1514:58324_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1430:59681_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:4838:62870_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19371:63360_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11964:65208_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15520:65730_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18899:69268_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14396:71434_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8959:72914_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14580:75541_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:3191:75765_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12223:77705_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17272:78197_1:N:0:ATCACG PGA_scaffold67687__1_contigs__length_62665 62571 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9827:89829_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19407:93355_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8538:93672_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15583:95741_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798939 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5215:96874_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6721:98602_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16139:98872_1:N:0:ATCACG PGA_scaffold71710__1_contigs__length_40502 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:17923:6154_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:19947:8931_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:15451:9779_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:16334:13051_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:19813:14141_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12852:16739_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:3113:19774_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:7519:21858_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:13246:24784_1:N:0:ATCACG PGA_scaffold48498__1_contigs__length_32874 32782 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:4462:29297_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:1185:29918_1:N:0:ATCACG PGA_scaffold67687__1_contigs__length_62665 62564 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:2916:31521_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:9444:36270_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:9001:39025_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:8259:39277_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 500000 reads; of these: 500000 (100.00%) were paired; of these: 291310 (58.26%) aligned concordantly 0 times 98673 (19.73%) aligned concordantly exactly 1 time 110017 (22.00%) aligned concordantly >1 times 41.74% overall alignment rate 500000 reads; of these: 500000 (100.00%) were paired; of these: 292741 (58.55%) aligned concordantly 0 times 97403 (19.48%) aligned concordantly exactly 1 time 109856 (21.97%) aligned concordantly >1 times 41.45% overall alignment rate Processed 500000 sequences in total Successfully deleted the temporary files pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 500000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 7681712 Total methylated C's in CpG context: 250800 Total methylated C's in CHG context: 34031 Total methylated C's in CHH context: 61819 Total methylated C's in Unknown context: 1183 Total unmethylated C's in CpG context: 839840 Total unmethylated C's in CHG context: 1579285 Total unmethylated C's in CHH context: 4915937 Total unmethylated C's in Unknown context: 14929 C methylated in CpG context: 23.0% C methylated in CHG context: 2.1% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 7.3% Bismark completed in 0d 0h 6m 2s ==================== Bismark run complete ====================