%%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 Jan 2 06:34:30 PST 2019
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 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: 2925.866
BogoMIPS: 5851.93
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 kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 7.9G 1.2G 1.2G 61G 61G
Swap: 4.7G 35M 4.6G
No LSB modules are available.
%%bash
mkdir /home/sam/data/virginica
mkdir /home/sam/analyses/20190103_Cvirginica_vcf_splitting
mkdir: cannot create directory ‘/home/sam/data/virginica’: File exists mkdir: cannot create directory ‘/home/sam/analyses/20190103_Cvirginica_vcf_splitting’: File exists
%env vcf_dir=/home/sam/data/virginica
%env wd=/home/sam/analyses/20190103_Cvirginica_vcf_splitting
%env bcftools=/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools
%env bgzip=/home/sam/software/bin/bgzip
%env tabix=/home/sam/software/bin/tabix
env: vcf_dir=/home/sam/data/virginica env: wd=/home/sam/analyses/20190103_Cvirginica_vcf_splitting env: bcftools=/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools env: bgzip=/home/sam/software/bin/bgzip env: tabix=/home/sam/software/bin/tabix
%%bash
${bcftools} --version
${bgzip} --version
${tabix} --version
bcftools 1.9-62-g1ce0f47 Using htslib 1.9-44-g80f3557 Copyright (C) 2018 Genome Research Ltd. License Expat: The MIT/Expat license This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. bgzip (htslib) 1.9-44-g80f3557 Copyright (C) 2018 Genome Research Ltd. tabix (htslib) 1.9-44-g80f3557 Copyright (C) 2018 Genome Research Ltd.
%%bash
cd ${vcf_dir}
rsync \
--archive \
--verbose \
--progress \
gannet:/volume1/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz .
# Uncomment line below to download via web
# wget http://gannet.fish.washington.edu/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz
ls -lh
receiving incremental file list total 0
ERROR: module is write only rsync error: syntax or usage error (code 1) at main.c(782) [sender=3.0.9] rsync: connection unexpectedly closed (110 bytes received so far) [Receiver] rsync error: error in rsync protocol data stream (code 12) at io.c(226) [Receiver=3.1.1]
%%bash
cd ${vcf_dir}
rsync \
--archive \
--verbose \
--progress \
gannet:/volume1/web/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz .
# Uncomment line below to download via web
# wget http://gannet.fish.washington.edu/seashell/eog_v2/VCF_files/Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz
ls -lh
receiving incremental file list Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz 32,645,951,849 100% 82.68MB/s 0:06:16 (xfr#1, to-chk=0/1) sent 30 bytes received 32,649,937,077 bytes 86,489,899.62 bytes/sec total size is 32,645,951,849 speedup is 1.00 total 31G -rwxrwxrwx 1 sam users 31G Dec 19 22:03 Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz
%%bash
cd ${vcf_dir}
time \
gunzip Combined.SNP.TRSdp5g95FnDNAmaf05.vcf.gz
ls -lh
total 186G -rwxrwxrwx 1 sam users 186G Dec 19 22:03 Combined.SNP.TRSdp5g95FnDNAmaf05.vcf
real 49m37.000s user 20m21.120s sys 2m30.532s
%%bash
time \
awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1 -k2,2n"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\
${bgzip} \
--threads 18 \
> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz
awk: cannot open Combined.SNP.TRSdp5g95FnDNAmaf05.vcf (No such file or directory) real 0m0.098s user 0m0.004s sys 0m0.000s
%%bash
cd ${vcf_dir}
time \
awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1 -k2,2n"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\
${bgzip} \
--threads 18 \
> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz
sort: write failed: /tmp/sortDMZSYb: No space left on device real 26m25.034s user 3m37.928s sys 1m59.788s
No space??
%%bash
df -h
Filesystem Size Used Avail Use% Mounted on udev 36G 0 36G 0% /dev tmpfs 7.1G 722M 6.4G 10% /run /dev/sda6 224G 80G 133G 38% / tmpfs 36G 221M 36G 1% /dev/shm tmpfs 5.0M 4.0K 5.0M 1% /run/lock tmpfs 36G 0 36G 0% /sys/fs/cgroup /dev/sdb1 917G 508G 363G 59% /home cgmfs 100K 0 100K 0% /run/cgmanager/fs tmpfs 7.1G 168K 7.1G 1% /run/user/1000 //owl.fish.washington.edu/web 51T 48T 2.8T 95% /mnt/owl
Deleted some stuff...
%%bash
df -h
Filesystem Size Used Avail Use% Mounted on udev 36G 0 36G 0% /dev tmpfs 7.1G 722M 6.4G 10% /run /dev/sda6 224G 80G 133G 38% / tmpfs 36G 250M 36G 1% /dev/shm tmpfs 5.0M 4.0K 5.0M 1% /run/lock tmpfs 36G 0 36G 0% /sys/fs/cgroup /dev/sdb1 917G 212G 659G 25% /home cgmfs 100K 0 100K 0% /run/cgmanager/fs tmpfs 7.1G 168K 7.1G 1% /run/user/1000 //owl.fish.washington.edu/web 51T 48T 2.8T 95% /mnt/owl
%%bash
cd ${vcf_dir}
time \
awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1 -k2,2n"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\
${bgzip} \
--threads 18 \
> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz
sort: write failed: /tmp/sortrHTYQb: No space left on device real 30m51.276s user 3m39.152s sys 1m58.672s
Ran out of space - again. Duh. Just realized the space limitation was in /tmp. Deleting the other files I previously removed had no effect.
Need to fix this...
%%bash
cd ${vcf_dir}
time \
awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort --temporary-directory=/home/sam/Downloads -k1,1 -k2,2n"}' Combined.SNP.TRSdp5g95FnDNAmaf05.vcf |\
${bgzip} \
--threads 18 \
> ${wd}/Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz
real 306m21.798s user 118m7.088s sys 30m32.388s
tabix¶%%bash
cd ${wd}
time \
${tabix} --preset vcf Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz
ls -lh
total 33G -rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz -rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi
real 19m46.280s user 18m55.812s sys 0m22.376s
%%bash
cd ${wd}
export BCFTOOLS_PLUGINS=/home/sam/software/bcftools-1.9-62-g1ce0f47/plugins
time \
${bcftools} plugin fill-AN-AC Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz \
--output-type z \
--threads 18 \
--output Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz
ls -lh
total 66G -rw-rw-r-- 1 sam sam 33G Jan 2 17:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz -rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz -rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi
real 109m50.921s user 210m56.972s sys 1m53.408s
%%bash
cd ${wd}
for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do
for sample in $($bcftools query -l $file); do
bcftools view \
--min-ac 1 \
--output-type z \
--samples $sample \
--output-file ${file/.vcf*/.$sample.vcf.gz} \
--threads 18 \
${file}
done
done
bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found
%%bash
cd ${wd}
for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do
for sample in `$bcftools query -l $file`; do
bcftools view \
--min-ac 1 \
--output-type z \
--samples $sample \
--output-file ${file/.vcf*/.$sample.vcf.gz} \
--threads 18 \
${file}
done
done
bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found
%%bash
cd ${wd}
for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do
for sample in $(/home/sam/software/bcftools-1.9-62-g1ce0f47/bcftools query -l $file); do
bcftools view \
--min-ac 1 \
--output-type z \
--samples $sample \
--output-file ${file/.vcf*/.$sample.vcf.gz} \
--threads 18 \
${file}
done
done
bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found bash: line 5: bcftools: command not found
%%bash
cd ${wd}
for file in Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz; do
for sample in $($bcftools query -l $file); do
${bcftools} view \
--min-ac 1 \
--output-type z \
--samples $sample \
--output-file ${file/.vcf*/.$sample.vcf.gz} \
--threads 18 \
${file}
done
done
%%bash
# Copy data to Gannet
cd /home/sam/analyses
time \
rsync \
--archive \
--relative \
./20190103_Cvirginica_vcf_splitting gannet:/volume1/web/Atumefaciens
real 21m56.303s user 14m55.344s sys 4m17.120s
%%bash
ls -lhtr ${wd}
total 113G -rw-rw-r-- 1 sam sam 33G Jan 2 14:43 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz -rw-rw-r-- 1 sam sam 538K Jan 2 15:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.vcf.gz.tbi -rw-rw-r-- 1 sam sam 33G Jan 2 17:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.vcf.gz -rw-rw-r-- 1 sam sam 567M Jan 2 20:28 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_1.vcf.gz -rw-rw-r-- 1 sam sam 586M Jan 2 21:32 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_2.vcf.gz -rw-rw-r-- 1 sam sam 588M Jan 2 22:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_3.vcf.gz -rw-rw-r-- 1 sam sam 560M Jan 2 23:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_4.vcf.gz -rw-rw-r-- 1 sam sam 549M Jan 3 00:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_5.vcf.gz -rw-rw-r-- 1 sam sam 572M Jan 3 01:50 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CL_6.vcf.gz -rw-rw-r-- 1 sam sam 527M Jan 3 02:54 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_1.vcf.gz -rw-rw-r-- 1 sam sam 530M Jan 3 03:58 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_2.vcf.gz -rw-rw-r-- 1 sam sam 541M Jan 3 05:02 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_3.vcf.gz -rw-rw-r-- 1 sam sam 534M Jan 3 06:05 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_4.vcf.gz -rw-rw-r-- 1 sam sam 540M Jan 3 07:09 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_5.vcf.gz -rw-rw-r-- 1 sam sam 540M Jan 3 08:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CLP_6.vcf.gz -rw-rw-r-- 1 sam sam 531M Jan 3 09:17 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_1.vcf.gz -rw-rw-r-- 1 sam sam 527M Jan 3 10:21 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_2.vcf.gz -rw-rw-r-- 1 sam sam 502M Jan 3 11:25 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_3.vcf.gz -rw-rw-r-- 1 sam sam 528M Jan 3 12:30 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_5.vcf.gz -rw-rw-r-- 1 sam sam 524M Jan 3 13:35 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_6.vcf.gz -rw-rw-r-- 1 sam sam 530M Jan 3 14:38 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.CS_7.vcf.gz -rw-rw-r-- 1 sam sam 552M Jan 3 15:42 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_1.vcf.gz -rw-rw-r-- 1 sam sam 568M Jan 3 16:47 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_2.vcf.gz -rw-rw-r-- 1 sam sam 557M Jan 3 17:50 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_3.vcf.gz -rw-rw-r-- 1 sam sam 524M Jan 3 18:54 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_4.vcf.gz -rw-rw-r-- 1 sam sam 562M Jan 3 19:58 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_5.vcf.gz -rw-rw-r-- 1 sam sam 545M Jan 3 21:02 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.DEBY_6.vcf.gz -rw-rw-r-- 1 sam sam 530M Jan 3 22:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_1.vcf.gz -rw-rw-r-- 1 sam sam 522M Jan 3 23:10 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_3.vcf.gz -rw-rw-r-- 1 sam sam 532M Jan 4 00:14 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_4.vcf.gz -rw-rw-r-- 1 sam sam 535M Jan 4 01:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_5.vcf.gz -rw-rw-r-- 1 sam sam 518M Jan 4 02:22 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_6.vcf.gz -rw-rw-r-- 1 sam sam 552M Jan 4 03:26 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_7.vcf.gz -rw-rw-r-- 1 sam sam 532M Jan 4 04:29 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_1.vcf.gz -rw-rw-r-- 1 sam sam 535M Jan 4 05:33 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_2.vcf.gz -rw-rw-r-- 1 sam sam 525M Jan 4 06:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_3.vcf.gz -rw-rw-r-- 1 sam sam 529M Jan 4 07:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_4.vcf.gz -rw-rw-r-- 1 sam sam 528M Jan 4 08:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_5.vcf.gz -rw-rw-r-- 1 sam sam 533M Jan 4 09:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HC_VA_6.vcf.gz -rw-rw-r-- 1 sam sam 252M Jan 4 10:52 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG0F2.vcf.gz -rw-rw-r-- 1 sam sam 228M Jan 4 11:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG2F1.vcf.gz -rw-rw-r-- 1 sam sam 194M Jan 4 13:00 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HG_HG2M5.vcf.gz -rw-rw-r-- 1 sam sam 525M Jan 4 14:04 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_1.vcf.gz -rw-rw-r-- 1 sam sam 524M Jan 4 15:08 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_2.vcf.gz -rw-rw-r-- 1 sam sam 530M Jan 4 16:13 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_3.vcf.gz -rw-rw-r-- 1 sam sam 526M Jan 4 17:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_4.vcf.gz -rw-rw-r-- 1 sam sam 515M Jan 4 18:20 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_5.vcf.gz -rw-rw-r-- 1 sam sam 519M Jan 4 19:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.HI_6.vcf.gz -rw-rw-r-- 1 sam sam 610M Jan 4 20:28 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_1_pool.vcf.gz -rw-rw-r-- 1 sam sam 619M Jan 4 21:32 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_3.vcf.gz -rw-rw-r-- 1 sam sam 637M Jan 4 22:36 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_4.vcf.gz -rw-rw-r-- 1 sam sam 668M Jan 4 23:42 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_7.vcf.gz -rw-rw-r-- 1 sam sam 598M Jan 5 00:47 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LM_8.vcf.gz -rw-rw-r-- 1 sam sam 590M Jan 5 01:51 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_1.vcf.gz -rw-rw-r-- 1 sam sam 579M Jan 5 02:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_2.vcf.gz -rw-rw-r-- 1 sam sam 577M Jan 5 04:00 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_3.vcf.gz -rw-rw-r-- 1 sam sam 589M Jan 5 05:04 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_4.vcf.gz -rw-rw-r-- 1 sam sam 576M Jan 5 06:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_5.vcf.gz -rw-rw-r-- 1 sam sam 576M Jan 5 07:13 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.LOLA_6.vcf.gz -rw-rw-r-- 1 sam sam 510M Jan 5 08:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_1.vcf.gz -rw-rw-r-- 1 sam sam 482M Jan 5 09:20 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_2.vcf.gz -rw-rw-r-- 1 sam sam 498M Jan 5 10:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_3.vcf.gz -rw-rw-r-- 1 sam sam 517M Jan 5 11:27 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_4.vcf.gz -rw-rw-r-- 1 sam sam 490M Jan 5 12:31 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_5.vcf.gz -rw-rw-r-- 1 sam sam 501M Jan 5 13:35 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NEH_6.vcf.gz -rw-rw-r-- 1 sam sam 515M Jan 5 14:40 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH0H4.vcf.gz -rw-rw-r-- 1 sam sam 450M Jan 5 15:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2F6.vcf.gz -rw-rw-r-- 1 sam sam 457M Jan 5 16:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2F8.vcf.gz -rw-rw-r-- 1 sam sam 473M Jan 5 17:51 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.NG_NH2M1.vcf.gz -rw-rw-r-- 1 sam sam 585M Jan 5 18:55 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_1.vcf.gz -rw-rw-r-- 1 sam sam 587M Jan 5 19:59 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_2.vcf.gz -rw-rw-r-- 1 sam sam 593M Jan 5 21:03 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_3.vcf.gz -rw-rw-r-- 1 sam sam 572M Jan 5 22:08 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_4.vcf.gz -rw-rw-r-- 1 sam sam 574M Jan 5 23:11 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_5.vcf.gz -rw-rw-r-- 1 sam sam 599M Jan 6 00:16 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.OBOYS2_6.vcf.gz -rw-rw-r-- 1 sam sam 584M Jan 6 01:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_1.vcf.gz -rw-rw-r-- 1 sam sam 568M Jan 6 02:23 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_2.vcf.gz -rw-rw-r-- 1 sam sam 586M Jan 6 03:27 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_3.vcf.gz -rw-rw-r-- 1 sam sam 572M Jan 6 04:30 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_4.vcf.gz -rw-rw-r-- 1 sam sam 586M Jan 6 05:34 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_5.vcf.gz -rw-rw-r-- 1 sam sam 581M Jan 6 06:38 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SL_6.vcf.gz -rw-rw-r-- 1 sam sam 528M Jan 6 07:41 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_10.vcf.gz -rw-rw-r-- 1 sam sam 517M Jan 6 08:45 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_11.vcf.gz -rw-rw-r-- 1 sam sam 523M Jan 6 09:48 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_12.vcf.gz -rw-rw-r-- 1 sam sam 531M Jan 6 10:53 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_7.vcf.gz -rw-rw-r-- 1 sam sam 522M Jan 6 11:56 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_8.vcf.gz -rw-rw-r-- 1 sam sam 523M Jan 6 12:59 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.SM_9.vcf.gz -rw-rw-r-- 1 sam sam 514M Jan 6 14:03 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_1.vcf.gz -rw-rw-r-- 1 sam sam 533M Jan 6 15:07 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_2.vcf.gz -rw-rw-r-- 1 sam sam 549M Jan 6 16:12 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_3.vcf.gz -rw-rw-r-- 1 sam sam 548M Jan 6 17:15 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_4.vcf.gz -rw-rw-r-- 1 sam sam 530M Jan 6 18:19 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_5.vcf.gz -rw-rw-r-- 1 sam sam 534M Jan 6 19:22 Combined.SNP.TRSdp5g95FnDNAmaf05.sorted.ANACfill.UMFS_6.vcf.gz