-----------------------
Start of variable list:
-----------------------
Sample_ID:
3_Liver_High_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 11:57:37 EDT 2019
Running on node : scc-kb6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500902
Current job name : Step_02_3_Liver_High_20
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500902.1.linga

Loading required modules...


List files in scratch directory:

total 641M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:00 .
drwxrwxrwt. 15 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:00 3_Liver_High_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 320M Jul  3 11:59 SRR7585234_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 321M Jul  3 12:00 SRR7585234_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585234_1.fastq <==
@SRR7585234.1 SN363:873:H7VCKBCXX:2:1101:1175:2190/1
GCTATGTGCACCATTTACACAAAATCAGCACTATTCTTTTCGCATGTCCG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585234.2 SN363:873:H7VCKBCXX:2:1101:1327:2206/1
CCAGGGATGCCCTGAGCTCCTCGATCTCAGCCTGCATCAGGTTGGCTCTG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIH
@SRR7585234.3 SN363:873:H7VCKBCXX:2:1101:1815:2051/1
ATTAAAATACACAGAACAAAATATCTGAGGTATAAGATAAAAAATGTAAT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585234.4 SN363:873:H7VCKBCXX:2:1101:2589:2209/1
GCCAAGTCCTTTGAGTTTTAAGCTATGGCTAGTAGTTCTCTGGCAAATAG
+
DDDDDIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585234.5 SN363:873:H7VCKBCXX:2:1101:2779:2105/1
CATAGAGATCCAACTGCCTCTGCCTCCAGAGTGCTGGGATCAAAGGGTGT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

==> SRR7585234_2.fastq <==
@SRR7585234.1 SN363:873:H7VCKBCXX:2:1101:1175:2190/2
CAACATAGGCTCTTCAAAAATTATGGTTTTGTCGGACATGCGAAAAGAAT
+
DDDDDHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIIIIIIIICGG
@SRR7585234.2 SN363:873:H7VCKBCXX:2:1101:1327:2206/2
ACGATGCTCTCAGAGGCCAGGACGACCTGAAAGAGCAGCTGGCCATGGTT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIGH
@SRR7585234.3 SN363:873:H7VCKBCXX:2:1101:1815:2051/2
NGAGGCCTGAGTGTTGCATCACATGCAGTAGGACATCATGTTAGCAACTC
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIF
@SRR7585234.4 SN363:873:H7VCKBCXX:2:1101:2589:2209/2
TAAATAGAATTAAAATCCAACTTATATGTGAAAATTCATTGTTAGGACCT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIIIHI
@SRR7585234.5 SN363:873:H7VCKBCXX:2:1101:2779:2105/2
ACTGAATTTGTGTTATATGTTGTTTTGCACAAGGGGCTGGGCCTTGGGGC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Starting FASTQC command


Processing SRR7585234_1.fastq

Printing command:
fastqc --outdir SRR7585234_1.fastq

Analysis complete for SRR7585234_1.fastq

Processing SRR7585234_2.fastq

Printing command:
fastqc --outdir SRR7585234_2.fastq

Analysis complete for SRR7585234_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.8G
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:01 .
drwxrwxrwt. 10 root     root      4.0K Jul  3 12:04 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:05 3_Liver_High_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.4G Jul  3 11:59 SRR7585234_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.4G Jul  3 12:00 SRR7585234_2.fastq
==========================================================
Finished on : Wed Jul  3 12:05:18 EDT 2019
0 hours, 7 minutes and 41 seconds elapsed.
==========================================================