-----------------------
Start of variable list:
-----------------------
Sample_ID:
5_Liver_Low_20
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE117741
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Jul  3 11:57:36 EDT 2019
Running on node : scc-kb5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500913
Current job name : Step_02_5_Liver_Low_20
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500913.1.linga

Loading required modules...


List files in scratch directory:

total 564M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:00 .
drwxrwxrwt. 12 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:00 5_Liver_Low_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 282M Jul  3 11:59 SRR7585257_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 282M Jul  3 12:00 SRR7585257_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585257_1.fastq <==
@SRR7585257.1 SN363:873:H7VCKBCXX:1:1102:1648:2071/1
NACAGACGTAGAGGAGATCGGAAGAGCACACGTCTGAACTCCCAGTCACA
+
#<<D@?CEEEH@FHIH@GGHHGEEGEHIIEFHC1<C1<D@<DEC<D@GEE
@SRR7585257.2 SN363:873:H7VCKBCXX:1:1102:2233:2096/1
TGAGAAGGCCAAGGAGGATCTGGCTAAGTCAGAGGCAAAAAGGAGATCGG
+
DDDDDIIIIIIIIIIIIHIHIIIIIIHIHHHIIIIIIIIIIIIHHHIIHH
@SRR7585257.3 SN363:873:H7VCKBCXX:1:1102:2269:2132/1
AGAGGATTCTGTAAAGCCTGGTGCCCATTTAACGGTGAAGAAAGTTTTTG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIHIHHIIII
@SRR7585257.4 SN363:873:H7VCKBCXX:1:1102:4384:2156/1
CGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCGGCTC
+
DD0DDHHHIIIIIHIIIHHHHIHIDHIIIIHIGHHHIIIIHICHIDDDHH
@SRR7585257.5 SN363:873:H7VCKBCXX:1:1102:5602:2146/1
AGTACAAATTCGGTCACACTAAGGTTTTCTTTAAAGCCGGCCTGTTGGGA
+
DDDDDIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIII

==> SRR7585257_2.fastq <==
@SRR7585257.1 SN363:873:H7VCKBCXX:1:1102:1648:2071/2
CCTCTACGTCTGTTGATCGTCGGACTGTAGAACTCTGAACGTGTAGATCT
+
<DDDDIIIIIIIIHHIHHHIIIIIIHIIIIIIIIIIIIHIIIIIIIIIII
@SRR7585257.2 SN363:873:H7VCKBCXX:1:1102:2233:2096/2
CCTTTTTGCCTCTGACTTAGCCAGATCCTCCTTGGCCTTCTCAGATCGTC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585257.3 SN363:873:H7VCKBCXX:1:1102:2269:2132/2
CCACCAACAAAAACTTTCTTCACCGTTAAATGGGCACCAGGCTTTACAGA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIII
@SRR7585257.4 SN363:873:H7VCKBCXX:1:1102:4384:2156/2
GGAAGAGCCGACATCGAAGGATCAAAAAGCGACGTCGCTATGAACGCTTG
+
DDDDCIHIHIIIIHIIHIIHFHHIIHIIIIIIIIHICHIIIIIIIHIHHI
@SRR7585257.5 SN363:873:H7VCKBCXX:1:1102:5602:2146/2
CGCATCTCCTCTAGAGTTCCCAACAGGCCGGCTTTAAAGAAAACCTTAGT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH

Starting FASTQC command


Processing SRR7585257_1.fastq

Printing command:
fastqc --outdir SRR7585257_1.fastq

Analysis complete for SRR7585257_1.fastq

Processing SRR7585257_2.fastq

Printing command:
fastqc --outdir SRR7585257_2.fastq

Analysis complete for SRR7585257_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.5G
drwx------  3 varsha97 waxmanlab 4.0K Jul  3 12:01 .
drwxrwxrwt. 9 root     root      4.0K Jul  3 12:02 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 12:02 5_Liver_Low_20_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.3G Jul  3 11:59 SRR7585257_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 1.3G Jul  3 12:00 SRR7585257_2.fastq
==========================================================
Finished on : Wed Jul  3 12:02:54 EDT 2019
0 hours, 5 minutes and 18 seconds elapsed.
==========================================================