%%bash
mkdir /home/sam/analyses/20180709_oly_methylseq
Genome preparation had previously been run:
The following command completed in 19,756 minutes (or, 13.7 days)!
%%bash
time \
/home/shared/Bismark-0.19.1/bismark \
--path_to_bowtie /home/shared/bowtie2-2.3.4.1-linux-x86_64/ \
--genome /home/sam/data/oly_methylseq/20180503_oly_genome_pbjelly_sjw_01_bismark \
-p 16 \
--non_directional \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/1_ATCACG_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/2_CGATGT_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/3_TTAGGC_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/4_TGACCA_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/5_ACAGTG_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/6_GCCAAT_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/7_CAGATC_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/8_ACTTGA_L001_R1_001_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_10_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_11_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_12_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_13_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_14_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_15_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_16_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_17_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_18_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_1_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_2_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_3_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_4_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_5_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_6_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_7_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_8_s456_trimmed.fq.gz \
/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_9_s456_trimmed.fq.gz \
1> /home/sam/analyses/20180709_oly_methylseq/20180709_bismark_01.out
2> /home/sam/analyses/20180709_oly_methylseq/20180709_bismark_01.err
sed '/^Subject:/ s/ / bismark JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
%%bash
ls
%%bash
mv *bt2* /home/sam/analyses/20180709_oly_methylseq/
ls -lh /home/sam/analyses/20180709_oly_methylseq/
total 21G -rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err -rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out -rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt
mv: cannot stat '*bt2*': No such file or directory
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
time \
/home/shared/Bismark-0.19.1/deduplicate_bismark \
--bam \
--single \
*.bam \
1> 20180805_dedup.out \
2> 20180805_dedup.err
sed '/^Subject:/ s/ / deduplication JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 132m33.812s user 254m16.060s sys 4m15.860s
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
ls -lh
total 35G -rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 213M Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err -rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out -rw-rw-r-- 1 sam sam 16K Aug 6 15:10 20180805_dedup.err -rw-rw-r-- 1 sam sam 849M Aug 6 15:10 20180805_dedup.out -rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 261M Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 259M Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 260M Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 271M Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 270M Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 233M Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 307M Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 520M Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 478M Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 776M Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 648M Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 829M Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 295 Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 626M Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 690M Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 457M Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 690M Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 588M Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 591M Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 601M Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 550M Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 292 Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 673M Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 674M Aug 6 14:50 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:50 zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 617M Aug 6 14:56 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:56 zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 491M Aug 6 15:01 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 292 Aug 6 15:01 zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 945M Aug 6 15:10 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 15:10 zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
time \
/home/shared/Bismark-0.19.1/bismark_methylation_extractor \
--bedgraph \
--counts \
--scaffolds \
--remove_spaces \
--multicore 16 \
--buffer_size 75% \
*deduplicated.bam \
1> 20180806_methyl_extraction.out \
2> 20180806_methyl_extraction.err
sed '/^Subject:/ s/ / methyl extraction JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 120m22.874s user 911m12.688s sys 191m7.556s
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
time \
/home/shared/Bismark-0.19.1/bismark2report \
1>20180813_bismark2report.out \
2>20180813_bismark2report.err
sed '/^Subject:/ s/ / bismark2report JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 0m0.897s user 0m0.404s sys 0m0.096s
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
ls -ltr *.html
-rw-rw-r-- 1 sam sam 353734 Aug 13 15:02 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353746 Aug 13 15:02 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353742 Aug 13 15:02 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353743 Aug 13 15:02 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353765 Aug 13 15:02 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353768 Aug 13 15:02 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353736 Aug 13 15:02 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353769 Aug 13 15:02 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353853 Aug 13 15:02 zr1394_10_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353845 Aug 13 15:02 zr1394_11_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353821 Aug 13 15:02 zr1394_12_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353828 Aug 13 15:02 zr1394_13_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353831 Aug 13 15:02 zr1394_14_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353848 Aug 13 15:02 zr1394_15_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353845 Aug 13 15:02 zr1394_16_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353837 Aug 13 15:02 zr1394_17_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353821 Aug 13 15:02 zr1394_18_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_1_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353823 Aug 13 15:02 zr1394_2_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_3_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_4_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353819 Aug 13 15:02 zr1394_5_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353818 Aug 13 15:02 zr1394_6_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_7_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353822 Aug 13 15:02 zr1394_9_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 353816 Aug 13 15:02 zr1394_8_s456_trimmed_bismark_bt2_SE_report.html
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
time \
/home/shared/Bismark-0.19.1/bismark2summary \
1>20180813_bismark2summary.out \
2>20180813_bismark2summary.err
sed '/^Subject:/ s/ / bismark2summary JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 0m0.090s user 0m0.052s sys 0m0.004s
%%bash
cd /home/sam/analyses/20180709_oly_methylseq/
ls -ltrh
total 154G -rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam -rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt -rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out -rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err -rw-rw-r-- 1 sam sam 213M Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 261M Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 259M Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 260M Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 271M Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 270M Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 233M Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 307M Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 296 Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 520M Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 478M Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 776M Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 648M Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 829M Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 295 Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 626M Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 690M Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 457M Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 690M Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 294 Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 588M Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 591M Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 601M Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 550M Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 292 Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 673M Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam sam 674M Aug 6 14:50 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam sam 293 Aug 6 14:50 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zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 2.9K Aug 6 17:07 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 177M Aug 6 17:08 CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 153M Aug 6 17:08 CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 153M Aug 6 17:08 CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 176M Aug 6 17:08 CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 19M Aug 6 17:09 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 19M Aug 6 17:09 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 184M Aug 6 17:13 CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 184M Aug 6 17:13 CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 170M Aug 6 17:13 CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 169M Aug 6 17:13 CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 876M Aug 6 17:13 CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 873M Aug 6 17:13 CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 903M Aug 6 17:13 CHH_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 899M Aug 6 17:13 CHH_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 270M Aug 6 17:13 CHG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 269M Aug 6 17:13 CHG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 259M Aug 6 17:13 CHG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 257M Aug 6 17:13 CHG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 824 Aug 6 17:13 zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 2.9K Aug 6 17:13 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 184M Aug 6 17:13 CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 170M Aug 6 17:14 CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 169M Aug 6 17:14 CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 184M Aug 6 17:14 CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 24M Aug 6 17:15 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 24M Aug 6 17:15 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 161M Aug 6 17:19 CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 161M Aug 6 17:19 CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 155M Aug 6 17:19 CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 154M Aug 6 17:19 CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 880M Aug 6 17:19 CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 879M Aug 6 17:19 CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 930M Aug 6 17:19 CHH_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 926M Aug 6 17:19 CHH_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 256M Aug 6 17:19 CHG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 255M Aug 6 17:19 CHG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 258M Aug 6 17:19 CHG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 257M Aug 6 17:19 CHG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 824 Aug 6 17:19 zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 2.9K Aug 6 17:19 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 161M Aug 6 17:19 CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 155M Aug 6 17:19 CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 154M Aug 6 17:19 CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 161M Aug 6 17:20 CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 22M Aug 6 17:21 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 22M Aug 6 17:21 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 205M Aug 6 17:24 CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 204M Aug 6 17:24 CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 170M Aug 6 17:24 CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 169M Aug 6 17:24 CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 835M Aug 6 17:24 CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 832M Aug 6 17:24 CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 794M Aug 6 17:24 CHH_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 791M Aug 6 17:24 CHH_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 262M Aug 6 17:24 CHG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 261M Aug 6 17:24 CHG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 230M Aug 6 17:24 CHG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 229M Aug 6 17:24 CHG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 824 Aug 6 17:24 zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 2.9K Aug 6 17:24 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 205M Aug 6 17:25 CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 170M Aug 6 17:25 CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 169M Aug 6 17:25 CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 204M Aug 6 17:25 CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 21M Aug 6 17:26 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 22M Aug 6 17:26 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 161M Aug 6 17:29 CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 160M Aug 6 17:29 CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 143M Aug 6 17:29 CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 142M Aug 6 17:29 CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 642M Aug 6 17:29 CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 640M Aug 6 17:29 CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 649M Aug 6 17:29 CHH_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 647M Aug 6 17:29 CHH_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 203M Aug 6 17:29 CHG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 203M Aug 6 17:29 CHG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 191M Aug 6 17:29 CHG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 190M Aug 6 17:29 CHG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 822 Aug 6 17:29 zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 2.9K Aug 6 17:29 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 161M Aug 6 17:30 CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 143M Aug 6 17:30 CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 142M Aug 6 17:30 CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 160M Aug 6 17:30 CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 18M Aug 6 17:31 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 18M Aug 6 17:31 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 210M Aug 6 17:36 CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 210M Aug 6 17:36 CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 1.4G Aug 6 17:36 CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 1.2G Aug 6 17:36 CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 1.2G Aug 6 17:36 CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 320M Aug 6 17:36 CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 319M Aug 6 17:36 CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 268M Aug 6 17:36 CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 267M Aug 6 17:36 CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 1.4G Aug 6 17:36 CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 390M Aug 6 17:36 CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 390M Aug 6 17:36 CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt -rw-rw-r-- 1 sam sam 826 Aug 6 17:36 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt -rw-rw-r-- 1 sam sam 3.0K Aug 6 17:36 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt -rw-rw-r-- 1 sam sam 73K Aug 6 17:36 20180806_methyl_extraction.out -rw-rw-r-- 1 sam sam 268M Aug 6 17:37 CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 210M Aug 6 17:37 CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 210M Aug 6 17:37 CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 267M Aug 6 17:37 CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt -rw-rw-r-- 1 sam sam 26M Aug 6 17:39 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 27M Aug 6 17:39 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz -rw-rw-r-- 1 sam sam 919M Aug 6 17:39 20180806_methyl_extraction.err -rw-rw-r-- 1 sam sam 0 Aug 13 15:02 20180813_bismark2report.out -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_10_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_11_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_12_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_13_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_14_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_15_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_16_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_17_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_18_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_1_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_2_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_3_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_4_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_5_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_6_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_7_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_9_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_8_s456_trimmed_bismark_bt2_SE_report.html -rw-rw-r-- 1 sam sam 33K Aug 13 15:02 20180813_bismark2report.err -rw-rw-r-- 1 sam sam 0 Aug 13 15:05 20180813_bismark2summary.out -rw-rw-r-- 1 sam sam 4.2K Aug 13 15:05 bismark_summary_report.txt -rw-rw-r-- 1 sam sam 269K Aug 13 15:05 bismark_summary_report.html -rw-rw-r-- 1 sam sam 2.5K Aug 13 15:05 20180813_bismark2summary.err
sudo usage¶%%bash
ls /mnt/owl/Athaliana/20180709_oly_methylseq/
1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bedGraph.gz 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bismark.cov.gz 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.M-bias.txt 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated_splitting_report.txt 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 20180709_bismark_01.err 20180709_bismark_01.out 20180805_dedup.err 20180805_dedup.out 20180806_methyl_extraction.err 20180806_methyl_extraction.out 20180813_bismark2report.err 20180813_bismark2report.out 20180813_bismark2summary.err 20180813_bismark2summary.out 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bedGraph.gz 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CHH_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OB_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt CpG_OT_8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_10_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_11_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_12_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_13_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_14_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_15_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_16_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_17_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_18_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_1_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_2_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_3_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_4_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_5_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_6_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_7_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt zr1394_10_s456_trimmed_bismark_bt2.bam zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_10_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_10_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_10_s456_trimmed_bismark_bt2_SE_report.html zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt zr1394_11_s456_trimmed_bismark_bt2.bam zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_11_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_11_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_11_s456_trimmed_bismark_bt2_SE_report.html zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt zr1394_12_s456_trimmed_bismark_bt2.bam zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_12_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_12_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_12_s456_trimmed_bismark_bt2_SE_report.html zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt zr1394_13_s456_trimmed_bismark_bt2.bam zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_13_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_13_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_13_s456_trimmed_bismark_bt2_SE_report.html zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt zr1394_14_s456_trimmed_bismark_bt2.bam zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_14_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_14_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_14_s456_trimmed_bismark_bt2_SE_report.html zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt zr1394_15_s456_trimmed_bismark_bt2.bam zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_15_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_15_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_15_s456_trimmed_bismark_bt2_SE_report.html zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt zr1394_16_s456_trimmed_bismark_bt2.bam zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_16_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_16_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_16_s456_trimmed_bismark_bt2_SE_report.html zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt zr1394_17_s456_trimmed_bismark_bt2.bam zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_17_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_17_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_17_s456_trimmed_bismark_bt2_SE_report.html zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt zr1394_18_s456_trimmed_bismark_bt2.bam zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_18_s456_trimmed_bismark_bt2_SE_report.html zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt zr1394_1_s456_trimmed_bismark_bt2.bam zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_1_s456_trimmed_bismark_bt2_SE_report.html zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt zr1394_2_s456_trimmed_bismark_bt2.bam zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_2_s456_trimmed_bismark_bt2_SE_report.html zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt zr1394_3_s456_trimmed_bismark_bt2.bam zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_3_s456_trimmed_bismark_bt2_SE_report.html zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt zr1394_4_s456_trimmed_bismark_bt2.bam zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_4_s456_trimmed_bismark_bt2_SE_report.html zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt zr1394_5_s456_trimmed_bismark_bt2.bam zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_5_s456_trimmed_bismark_bt2_SE_report.html zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt zr1394_6_s456_trimmed_bismark_bt2.bam zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_6_s456_trimmed_bismark_bt2_SE_report.html zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt zr1394_7_s456_trimmed_bismark_bt2.bam zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_7_s456_trimmed_bismark_bt2_SE_report.html zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt zr1394_8_s456_trimmed_bismark_bt2.bam zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_8_s456_trimmed_bismark_bt2_SE_report.html zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt zr1394_9_s456_trimmed_bismark_bt2.bam zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_9_s456_trimmed_bismark_bt2_SE_report.html zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt
Used incorrect naming, so re-ran.
Then, killed after realizing I could set thread count to speed things up.
%%bash
cd /home/sam/analyses/20180709_oly_methylseq
time \
find *deduplicated.bam | \
xargs basename -s .bam | \
xargs -I{} /home/shared/samtools-1.8/samtools \
sort --threads 16 {}.bam \
-o {}.sorted.bam
sed '/^Subject:/ s/ / sorting JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
[bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... [bam_sort_core] merging from 0 files and 16 in-memory blocks... real 14m48.065s user 177m2.984s sys 1m58.888s
%%bash
cd /home/sam/analyses/20180709_oly_methylseq
ls *sorted*
1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam
The "-@ 16" below specifies number of CPU threads to use.
%%bash
cd /home/sam/analyses/20180709_oly_methylseq
find *.sorted.bam | \
xargs basename -s .sorted.bam | \
xargs -I{} /home/shared/samtools-1.8/samtools \
index -@ 16 {}.sorted.bam
sed '/^Subject:/ s/ / indexing JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
%%bash
cd /home/sam/analyses/20180709_oly_methylseq
ls *.bai
1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai
sudo requirement¶%%bash
ls -lh /mnt/owl/Athaliana/20180709_oly_methylseq/*sorted*
-rw-rw-r-- 1 sam users 209M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 27M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 254M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 252M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 254M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 264M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 263M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 227M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 27M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 298M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 454M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 419M Aug 16 09:52 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 693M Aug 16 09:53 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 31M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 565M Aug 16 09:53 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 723M Aug 16 09:54 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 32M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 542M Aug 16 09:55 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 600M Aug 16 09:56 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 30M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 400M Aug 16 09:56 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 26M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 611M Aug 16 09:57 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 529M Aug 16 09:58 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 533M Aug 16 09:58 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 29M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 543M Aug 16 09:59 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 492M Aug 16 10:00 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 28M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 613M Aug 16 10:00 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 32M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 617M Aug 16 10:01 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 31M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 551M Aug 16 10:02 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 29M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 440M Aug 16 10:02 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 27M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai -rw-rw-r-- 1 sam users 840M Aug 16 10:03 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam -rw-rw-r-- 1 sam users 33M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai