%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
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 Nov 20 11:53:55 PST 2019
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.6 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
swoose
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 44
Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Stepping: 2
CPU MHz: 2925.971
BogoMIPS: 5851.97
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 12288K
NUMA node0 CPU(s): 0-23
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 pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 39G 1.1G 969M 30G 29G
Swap: 4.7G 917M 3.8G
No LSB modules are available.
%env variables are good for passing to bash cells
# Set workding directory
%env wd=/home/sam/analyses/20191120_swoose_pgen_v074_renaming
wd="/home/sam/analyses/20191120_swoose_pgen_v074_renaming"
%env old_fa_index=Pgenerosa_v074.fa.fai
%env base_cov_url=https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed
env: wd=/home/sam/analyses/20191120_swoose_pgen_v074_renaming env: old_fa_index=Pgenerosa_v074.fa.fai env: base_cov_url=https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed
%%bash
echo ${wget_options}
--recursive --accept deduplicated.bismark.cov.gz --no-parent --no-directories --quietly --no-check-certificate
%%bash
mkdir --parents ${wd}
cd {wd}
/home/sam/analyses/20191120_swoose_pgen_v074_renaming
%%bash
url_array=("${base_cov_url}"/0807/ "${base_cov_url}"/0807-003/ "${base_cov_url}"/0807-004/ "${base_cov_url}"/0809-005/)
# Downlaod Bismark coverage files
for url in "${url_array[@]}"
do
echo "Downloading coverage files from ${url}"
wget \
--recursive \
--accept deduplicated.bismark.cov.gz \
--no-parent \
--no-directories \
--quiet \
--no-check-certificate \
"${url}"
done
# Remove index files
rm *.html*
# Download Pgen_074 FastA Index file
wget --quiet http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v074.fa.fai
ls -lh
Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807/ Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807-003/ Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807-004/ Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0809-005/ total 2.5G -rw-rw-r-- 1 sam sam 57M Aug 12 14:29 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 68M Aug 12 14:57 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 64M Aug 12 15:24 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 62M Aug 12 15:49 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 69M Aug 12 16:18 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 62M Aug 12 16:43 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 58M Aug 12 17:05 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Aug 12 17:29 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Aug 12 17:55 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 62M Aug 12 18:20 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 55M Aug 12 18:41 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Aug 12 19:05 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 49M Aug 7 08:39 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 53M Aug 7 09:00 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 44M Aug 7 09:16 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 47M Aug 7 09:32 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 36M Aug 7 09:43 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 53M Aug 7 10:04 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 44M Aug 7 10:17 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Aug 7 10:32 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 53M Aug 7 10:50 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 45M Aug 7 11:06 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Aug 7 11:21 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 49M Aug 7 11:37 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 53M Aug 8 05:03 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 63M Aug 8 05:28 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 53M Aug 8 05:49 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 62M Aug 8 06:15 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 44M Aug 8 06:29 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 25M Aug 8 06:36 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 47M Aug 8 06:53 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Aug 8 07:07 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 50M Aug 8 07:25 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 57M Aug 8 07:48 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 33M Aug 8 07:58 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 45M Aug 8 08:14 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 33M Aug 8 10:04 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Aug 8 10:19 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 51M Aug 8 10:37 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 54M Aug 8 10:58 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 55M Aug 8 11:19 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Aug 8 11:37 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 34M Aug 8 11:47 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 36M Aug 8 11:59 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 29M Aug 8 12:07 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 33M Aug 8 12:17 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Aug 8 12:30 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 47M Aug 8 12:47 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Aug 12 19:20 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 48M Aug 12 19:39 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Aug 12 19:54 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 31M Aug 12 20:04 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai
rm: cannot remove '*.html*': No such file or directory
%%bash
zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | head
PGA_scaffold1__77_contigs__length_89643857 54 54 0 0 1 PGA_scaffold1__77_contigs__length_89643857 72 72 0 0 1 PGA_scaffold1__77_contigs__length_89643857 96 96 0 0 1 PGA_scaffold1__77_contigs__length_89643857 119 119 0 0 1 PGA_scaffold1__77_contigs__length_89643857 202 202 0 0 1 PGA_scaffold1__77_contigs__length_89643857 209 209 0 0 1 PGA_scaffold1__77_contigs__length_89643857 213 213 0 0 1 PGA_scaffold1__77_contigs__length_89643857 221 221 0 0 1 PGA_scaffold1__77_contigs__length_89643857 238 238 0 0 1 PGA_scaffold1__77_contigs__length_89643857 1254 1254 0 0 1
%%bash
# Array of old scaffold names
# Uses first column of FastA index file to get scaffold names
mapfile -t orig_scaffold_names < <(awk '{print $1}' "${old_fa_index}")
# Array of new scaffold names
mapfile -t new_scaffold_names < <(for number in {01..18}; do echo "Scaffold_${number}"; done)
for gzfile in *cov.gz
do
# Save gunzipped filename (via parameter substitution - removes .gz from input filename)
name="${gzfile%.*}"
# Gunzip the gzipped file
echo ""
echo "Decompressing ${gzfile}"
echo "Generating ${name}"
gunzip "${gzfile}"
# sed substitution
# creates sed script to find original scaffold names and replace them with new scafold names
# and passes to sed via stdin
for index in "${!orig_scaffold_names[@]}"
do
printf "s/%s/%s/\n" "${orig_scaffold_names[index]}" "${new_scaffold_names[index]}"
done | sed --file - "${name}" \
>> "${name}".tmp
# Remove the gunzipped file, now that a .tmp file exists
echo ""
echo "Now removing ${name}"
rm "${name}"
# Compress .tmp coverage files
echo ""
echo "Compressing ${name}.tmp to ${name}.gz"
gzip --to-stdout "${name}".tmp > "${name}".gz
done
ls -ltrh
Decompressing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Decompressing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Generating EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Now removing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov Compressing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz total 19G -rw-rw-r-- 1 sam sam 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai -rw-rw-r-- 1 sam sam 380M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 56M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 440M Nov 20 13:47 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 66M Nov 20 13:48 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 416M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 63M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 404M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 61M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 445M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 67M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 404M Nov 20 13:52 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 61M Nov 20 13:53 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 380M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 57M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 394M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 59M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 392M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 59M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 400M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 60M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 363M Nov 20 13:58 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 54M Nov 20 13:59 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 395M Nov 20 13:59 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 59M Nov 20 14:00 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 323M Nov 20 14:00 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 48M Nov 20 14:01 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 347M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 52M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 289M Nov 20 14:02 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 43M Nov 20 14:03 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 312M Nov 20 14:03 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 46M Nov 20 14:04 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 244M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 35M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 346M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 52M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 294M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 43M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 288M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 42M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 354M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 52M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 300M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 44M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 283M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 42M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 326M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 48M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 346M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 51M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 408M Nov 20 14:13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 61M Nov 20 14:14 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 350M Nov 20 14:14 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 52M Nov 20 14:15 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 404M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 61M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 294M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 43M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 169M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 24M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 306M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 45M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 279M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 41M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 329M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 49M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 374M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 56M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 223M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 32M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 295M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 44M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 221M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 32M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 286M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 42M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 336M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 50M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 349M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 52M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 364M Nov 20 14:27 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 54M Nov 20 14:28 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 275M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 41M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 227M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 33M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 242M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 35M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 194M Nov 20 14:30 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 28M Nov 20 14:31 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 224M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 32M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 277M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 41M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 311M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 46M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 288M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 42M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 312M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 47M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 285M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 42M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 206M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp -rw-rw-r-- 1 sam sam 30M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
%%bash
zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | head
zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | tail
Scaffold_01 54 54 0 0 1 Scaffold_01 72 72 0 0 1 Scaffold_01 96 96 0 0 1 Scaffold_01 119 119 0 0 1 Scaffold_01 202 202 0 0 1 Scaffold_01 209 209 0 0 1 Scaffold_01 213 213 0 0 1 Scaffold_01 221 221 0 0 1 Scaffold_01 238 238 0 0 1 Scaffold_01 1254 1254 0 0 1 Scaffold_18 27722766 27722766 100 1 0 Scaffold_18 27722918 27722918 100 1 0 Scaffold_18 27722923 27722923 0 0 1 Scaffold_18 27722925 27722925 100 2 0 Scaffold_18 27726479 27726479 0 0 1 Scaffold_18 27726498 27726498 100 1 0 Scaffold_18 27727720 27727720 0 0 2 Scaffold_18 27727726 27727726 0 0 2 Scaffold_18 27727766 27727766 0 0 2 Scaffold_18 27730103 27730103 33.3333333333333 1 2
%%bash
rm *.tmp "${old_fa_index}"
ls -lh
total 2.4G -rw-rw-r-- 1 sam sam 56M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 66M Nov 20 13:48 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 63M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 67M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Nov 20 13:53 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 57M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 59M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 59M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 60M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 54M Nov 20 13:59 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 59M Nov 20 14:00 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 48M Nov 20 14:01 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 52M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Nov 20 14:03 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 46M Nov 20 14:04 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 35M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 52M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 52M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 44M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 48M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 51M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Nov 20 14:14 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 52M Nov 20 14:15 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 61M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 43M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 24M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 45M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 41M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 49M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 56M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 32M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 44M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 32M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 50M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 52M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 54M Nov 20 14:28 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 41M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 33M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 35M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 28M Nov 20 14:31 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 32M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 41M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 46M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 47M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 42M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz -rw-rw-r-- 1 sam sam 30M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz