%%bash
echo "TODAY'S DATE"
date
echo "------------"
echo ""
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "
hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE
Wed May 30 12:15:30 PDT 2018
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.4 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
emu
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 2
Core(s) per socket: 4
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 26
Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
Stepping: 5
CPU MHz: 2394.000
CPU max MHz: 2394.0000
CPU min MHz: 1596.0000
BogoMIPS: 4521.81
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 8192K
NUMA node0 CPU(s): 0-15
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm tpr_shadow vnmi flexpriority ept vpid dtherm ida
------------
Memory Specs
total used free shared buff/cache available
Mem: 47G 552M 40G 258M 6.0G 45G
Swap: 11G 0B 11G
No LSB modules are available.
%%bash
ls /home/sam/analyses/20180507_oly_methylseq_bismark/
1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 20180507_bismark_01.err 20180507_bismark_02.err 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt zr1394_10_s456_trimmed_bismark_bt2.bam zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt zr1394_11_s456_trimmed_bismark_bt2.bam zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt zr1394_12_s456_trimmed_bismark_bt2.bam zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt zr1394_13_s456_trimmed_bismark_bt2.bam zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt zr1394_14_s456_trimmed_bismark_bt2.bam zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt zr1394_15_s456_trimmed_bismark_bt2.bam zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt zr1394_16_s456_trimmed_bismark_bt2.bam zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt zr1394_17_s456_trimmed_bismark_bt2.bam zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt zr1394_18_s456_trimmed_bismark_bt2.bam zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt zr1394_1_s456_trimmed_bismark_bt2.bam zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt zr1394_2_s456_trimmed_bismark_bt2.bam zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt zr1394_3_s456_trimmed_bismark_bt2.bam zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt zr1394_4_s456_trimmed_bismark_bt2.bam zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt zr1394_5_s456_trimmed_bismark_bt2.bam zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt zr1394_6_s456_trimmed_bismark_bt2.bam zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt zr1394_7_s456_trimmed_bismark_bt2.bam zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt zr1394_8_s456_trimmed_bismark_bt2.bam zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt zr1394_9_s456_trimmed_bismark_bt2.bam zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt
%%bash
mkdir /home/sam/analyses/20180531_oly_bismark_deduplication
time \
/home/shared/Bismark-0.19.1/deduplicate_bismark \
--single \
--bam \
--samtools_path /home/shared/samtools-1.8/samtools \
--output_dir /home/sam/analyses/20180531_oly_bismark_deduplication \
/home/sam/analyses/20180531_oly_bismark_deduplication/*.bam \
1> /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stdout.txt \
2> /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stederr.txt
sed '/^Subject:/ s/ / deduplication JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
bash: line 5: /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stdout.txt: Not a directory real 0m0.001s user 0m0.000s sys 0m0.000s
%%bash
mkdir /home/sam/analyses/20180531_oly_bismark_deduplication
time \
/home/shared/Bismark-0.19.1/deduplicate_bismark \
--single \
--bam \
--samtools_path /home/shared/samtools-1.8/samtools \
--output_dir /home/sam/analyses/20180531_oly_bismark_deduplication \
/home/sam/analyses/20180507_oly_methylseq_bismark/*.bam \
1> /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stdout.txt \
2> /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stederr.txt
sed '/^Subject:/ s/ / deduplication JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
mkdir: cannot create directory ‘/home/sam/analyses/20180531_oly_bismark_deduplication’: File exists bash: line 5: /home/shared/Bismark-0.19.1/deduplicate_bismark/20180531_dedup_stdout.txt: Not a directory real 0m0.001s user 0m0.000s sys 0m0.000s
%%bash
time \
/home/shared/Bismark-0.19.1/deduplicate_bismark \
--single \
--bam \
--samtools_path /home/shared/samtools-1.8/samtools \
--output_dir /home/sam/analyses/20180531_oly_bismark_deduplication \
/home/sam/analyses/20180507_oly_methylseq_bismark/*.bam \
1> /home/sam/analyses/20180531_oly_bismark_deduplication/20180531_dedup_stdout.txt \
2> /home/sam/analyses/20180531_oly_bismark_deduplication/20180531_dedup_stederr.txt
sed '/^Subject:/ s/ / deduplication JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 6m49.106s user 9m58.688s sys 0m13.152s
%%bash
ls /home/sam/analyses/20180531_oly_bismark_deduplication
1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 20180531_dedup_stdout.txt 20180531_dedup_stederr.txt 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt
%%bash
tail /home/sam/analyses/20180531_oly_bismark_deduplication/20180531_dedup_stederr.txt
Output file is: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_9_s456_trimmed_bismark_bt2.bam: 345938 Total number duplicated alignments removed: 9557 (2.76%) Duplicated alignments were found at: 7288 different position(s) Total count of deduplicated leftover sequences: 336381 (97.24% of total)
%%bash
tail /home/sam/analyses/20180531_oly_bismark_deduplication/20180531_dedup_stdout.txt
skipping header line: @SQ SN:Contig696937 LN:102 skipping header line: @SQ SN:Contig696938 LN:104 skipping header line: @SQ SN:Contig696939 LN:221 skipping header line: @SQ SN:Contig696940 LN:107 skipping header line: @SQ SN:Contig696941 LN:107 skipping header line: @SQ SN:Contig696942 LN:160 skipping header line: @SQ SN:Contig696943 LN:108 skipping header line: @SQ SN:Contig696944 LN:127 skipping header line: @SQ SN:Contig696945 LN:171 skipping header line: @PG ID:Bismark VN:v0.19.1 CL:"bismark --path_to_bowtie /home/shared/bowtie2-2.3.4.1-linux-x86_64/ --genome /home/sam/data/oly_methylseq/oly_genome/ -u 1000000 -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"
%%bash
suffix="_trimmed_bismark_bt2.deduplicated.bam"
cd /home/sam/analyses/20180531_oly_bismark_deduplication/
time \
find . -name "*deduplicated.bam" \
| xargs basename -s "$suffix" \
| xargs -I {} /home/shared/samtools-1.8/samtools \
sort {}"$suffix"" \
-o {}_dedup.sorted.bam \
2> 20180531_samtools_stderr.txt
sed '/^Subject:/ s/ / samtools sorting JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
bash: line 13: unexpected EOF while looking for matching `"' bash: line 14: syntax error: unexpected end of file
%%bash
suffix="_trimmed_bismark_bt2.deduplicated.bam"
cd /home/sam/analyses/20180531_oly_bismark_deduplication/
time \
find . -name "*deduplicated.bam" \
| xargs basename -s "$suffix" \
| xargs -I{} /home/shared/samtools-1.8/samtools \
sort {}"$suffix"" \
-o {}_dedup.sorted.bam \
2> 20180531_samtools_stderr.txt
sed '/^Subject:/ s/ / samtools sorting JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
bash: line 13: unexpected EOF while looking for matching `"' bash: line 14: syntax error: unexpected end of file
Figured it out! Got jacked up by the autocompletion feature when typing parenthese or quotes! There's an extra " in the sort line!!
%%bash
suffix="_trimmed_bismark_bt2.deduplicated.bam"
cd /home/sam/analyses/20180531_oly_bismark_deduplication/
time \
find . -name "*deduplicated.bam" \
| xargs basename -s "$suffix" \
| xargs -I{} /home/shared/samtools-1.8/samtools \
sort {}"$suffix" \
-o {}_dedup.sorted.bam \
2> 20180531_samtools_stderr.txt
sed '/^Subject:/ s/ / samtools sorting JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 5m39.963s user 5m28.912s sys 0m2.168s
%%bash
cd /home/sam/analyses/20180531_oly_bismark_deduplication/
ls -ltr *sorted.bam
-rw-rw-r-- 1 sam sam 25197027 May 30 13:53 zr1394_5_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23630948 May 30 13:53 zr1394_4_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31590476 May 30 13:54 4_TGACCA_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31307068 May 30 13:54 2_CGATGT_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23768268 May 30 13:54 zr1394_8_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31150179 May 30 13:54 8_ACTTGA_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 24494495 May 30 13:55 zr1394_2_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31543876 May 30 13:55 1_ATCACG_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 22976097 May 30 13:55 zr1394_17_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 21297219 May 30 13:55 zr1394_11_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31321161 May 30 13:55 3_TTAGGC_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23793528 May 30 13:56 zr1394_1_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 22115792 May 30 13:56 zr1394_15_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 22004950 May 30 13:56 zr1394_16_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 22996512 May 30 13:56 zr1394_13_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31198018 May 30 13:56 5_ACAGTG_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31051100 May 30 13:57 6_GCCAAT_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 25355389 May 30 13:57 zr1394_12_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 24664288 May 30 13:57 zr1394_9_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 24698718 May 30 13:57 zr1394_18_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23071669 May 30 13:58 zr1394_10_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23713220 May 30 13:58 zr1394_7_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 31467088 May 30 13:58 7_CAGATC_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam sam 23521567 May 30 13:58 zr1394_3_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 22265093 May 30 13:58 zr1394_14_s456_dedup.sorted.bam -rw-rw-r-- 1 sam sam 25365395 May 30 13:59 zr1394_6_s456_dedup.sorted.bam
Had to use sudo to copy to owl, so copied outside of notebook.
%%bash
ls -lh /mnt/owl/Athaliana/20180531_oly_bismark_deduplication/
total 2.1G -rw-rw-r-- 1 sam users 31M May 30 13:55 1_ATCACG_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 31M May 30 12:37 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 341 May 30 12:37 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 849M May 30 12:43 20180531_dedup_stdout.txt -rw-rw-r-- 1 sam users 20K May 30 12:43 20180531_dedup_stederr.txt -rw-rw-r-- 1 sam users 0 May 30 13:53 20180531_samtools_stderr.txt -rw-rw-r-- 1 sam users 30M May 30 13:54 2_CGATGT_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 31M May 30 12:37 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:37 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 30M May 30 13:55 3_TTAGGC_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 31M May 30 12:37 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:37 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 31M May 30 13:54 4_TGACCA_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 31M May 30 12:38 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:38 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 30M May 30 13:56 5_ACAGTG_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 30M May 30 12:38 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:38 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 30M May 30 13:57 6_GCCAAT_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 30M May 30 12:38 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:38 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 31M May 30 13:58 7_CAGATC_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 31M May 30 12:38 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:38 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 30M May 30 13:54 8_ACTTGA_L001_R1_001_dedup.sorted.bam -rw-rw-r-- 1 sam users 30M May 30 12:39 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 340 May 30 12:39 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 1.1K May 30 14:29 readme.txt -rw-rw-r-- 1 sam users 23M May 30 13:58 zr1394_10_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:39 zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:39 zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 21M May 30 13:55 zr1394_11_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 21M May 30 12:39 zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:39 zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 25M May 30 13:57 zr1394_12_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 25M May 30 12:39 zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:39 zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 22M May 30 13:56 zr1394_13_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:40 zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:40 zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 22M May 30 13:58 zr1394_14_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 22M May 30 12:40 zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:40 zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 22M May 30 13:56 zr1394_15_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 22M May 30 12:40 zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:40 zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 21M May 30 13:56 zr1394_16_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 22M May 30 12:40 zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:40 zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 22M May 30 13:55 zr1394_17_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:41 zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 335 May 30 12:41 zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 24M May 30 13:57 zr1394_18_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 24M May 30 12:41 zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 334 May 30 12:41 zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 23M May 30 13:56 zr1394_1_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 24M May 30 12:41 zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:41 zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 24M May 30 13:55 zr1394_2_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 24M May 30 12:41 zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:41 zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 23M May 30 13:58 zr1394_3_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:42 zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:42 zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 23M May 30 13:53 zr1394_4_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:42 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:42 zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 25M May 30 13:53 zr1394_5_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 25M May 30 12:42 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 332 May 30 12:42 zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 25M May 30 13:59 zr1394_6_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 25M May 30 12:42 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 332 May 30 12:42 zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 23M May 30 13:58 zr1394_7_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 23M May 30 12:43 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:43 zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 23M May 30 13:54 zr1394_8_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 24M May 30 12:43 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 333 May 30 12:43 zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt -rw-rw-r-- 1 sam users 24M May 30 13:57 zr1394_9_s456_dedup.sorted.bam -rw-rw-r-- 1 sam users 24M May 30 12:43 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam -rw-rw-r-- 1 sam users 332 May 30 12:43 zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt