-----------------------
Start of variable list:
-----------------------
Sample_ID:
6_Liver_Low_3h
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-ka3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500922
Current job name : Step_02_6_Liver_Low_3h
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500922.1.linga

Loading required modules...


List files in scratch directory:

total 527M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 11:59 .
drwxrwxrwt. 14 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 11:59 6_Liver_Low_3h_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 264M Jul  3 11:58 SRR7585272_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 264M Jul  3 11:59 SRR7585272_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585272_1.fastq <==
@SRR7585272.1 SN363:873:H7VCKBCXX:2:1101:1758:2180/1
TCCTGTGAAAGGTCAGAATCCCCAGGCGCTGACCACCACAGAAGGGTCCA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIII
@SRR7585272.2 SN363:873:H7VCKBCXX:2:1101:2239:2190/1
TCCGCAGCTTGTCCCCCAGAAAATAGGAAAGCCAGAGTCTTCAACCCGGA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIII
@SRR7585272.3 SN363:873:H7VCKBCXX:2:1101:2455:2161/1
GGTAGTAGATCTTTACTGATGCCAGCACAGTTAGACAGATCACCTTGAAC
+
DDDDDIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585272.4 SN363:873:H7VCKBCXX:2:1101:2657:2054/1
CCTCATAGGGAGAGAAGGATGAAGGGGTATGCTATATATTTTGTTAGTGG
+
DDDDDIIIIIIIFIIIIHHHHIIIIIIHIIIIIIIIIIIIIIIIIIIIII
@SRR7585272.5 SN363:873:H7VCKBCXX:2:1101:2585:2055/1
GCATCTCTGGAGTGACAGGGGTTGGGGTGGCTTTCCCCACATTTTCTTTG
+
DDDDDIIIIIHIHHHIIIIIIIHIIIIIIIIHEHIIIIIIIIIIIIIIII

==> SRR7585272_2.fastq <==
@SRR7585272.1 SN363:873:H7VCKBCXX:2:1101:1758:2180/2
TAGAGCTTGGACCCTTCTGTGGTGGTCAGCGCCTGGGGATTCTGACCTTT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHIIIIIIIIIII
@SRR7585272.2 SN363:873:H7VCKBCXX:2:1101:2239:2190/2
CTGGTGCACTATGCGGGCACCGTGGACTACAACATTATTGGCTGGCTGGA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH
@SRR7585272.3 SN363:873:H7VCKBCXX:2:1101:2455:2161/2
GAGGCCTTGGCACACCCTTTCTTTCAGGAGTACGTAGTAGAAGAAGTACG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIII
@SRR7585272.4 SN363:873:H7VCKBCXX:2:1101:2657:2054/2
NATTCGCATCTCCATTATTCTAGACCCACTAACAAAATATATAGCATACC
+
#<<DDHHIIIIIIHIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585272.5 SN363:873:H7VCKBCXX:2:1101:2585:2055/2
NACCAAGAGAACTTTAGCTCGGTTTTGTACAAAGAAAATGTGGGGAAAGC
+
#<<DDHIIIIIIIIHIIHHIIIHIIIIIIIIIIIIIIIIIIIHIHHHIIG

Starting FASTQC command


Processing SRR7585272_1.fastq

Printing command:
fastqc --outdir SRR7585272_1.fastq

Analysis complete for SRR7585272_1.fastq

Processing SRR7585272_2.fastq

Printing command:
fastqc --outdir SRR7585272_2.fastq

Analysis complete for SRR7585272_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.3G
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:00 .
drwxrwxrwt. 14 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:01 6_Liver_Low_3h_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.2G Jul  3 11:58 SRR7585272_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.2G Jul  3 11:59 SRR7585272_2.fastq
==========================================================
Finished on : Wed Jul  3 12:01:42 EDT 2019
0 hours, 4 minutes and 6 seconds elapsed.
==========================================================