-----------------------
Start of variable list:
-----------------------
Sample_ID:
6_Liver_Basal_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-tm3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500918
Current job name : Step_02_6_Liver_Basal_20
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500918.1.linga

Loading required modules...


List files in scratch directory:

total 450M
drwx------  3 varsha97 waxmanlab 4.0K Jul  3 11:59 .
drwxrwxrwt. 7 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 11:59 6_Liver_Basal_20_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 225M Jul  3 11:58 SRR7585268_1.fastq.gz
-rw-r--r--  1 varsha97 waxmanlab 225M Jul  3 11:59 SRR7585268_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585268_1.fastq <==
@SRR7585268.1 SN363:854:H5VMFBCXX:2:1101:4080:2097/1
GGGTTGGTGTTCAGATACCCACAAATTTCACAGTTTCTGCTCCCAGCTAT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585268.2 SN363:854:H5VMFBCXX:2:1101:4701:2048/1
GGATTTCGGGTACAGCCCCACCACGGTCTCATTCAGGGGGTCCTTGTTCT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIII
@SRR7585268.3 SN363:854:H5VMFBCXX:2:1101:5594:2101/1
TGTAGAGTTTTTGTAGTACGTTATTATCTTTTTTTAGGTGGATCGTCGGA
+
DDDDDIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIHIHIIIIIHH
@SRR7585268.4 SN363:854:H5VMFBCXX:2:1101:7631:2046/1
TGACAGGTAGTTCTCCTTCTCAGATTCTCAGCGGCTTTCCTCTTTCTCCA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585268.5 SN363:854:H5VMFBCXX:2:1101:9001:2112/1
ACTATATGAGGTTACGTTTGTTCAGGTTTTTTTAGGGCTTGATAGTCAGG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

==> SRR7585268_2.fastq <==
@SRR7585268.1 SN363:854:H5VMFBCXX:2:1101:4080:2097/2
TAAAGAAGATCTATCTCAGAGGCTATAGCTGGGAGCAGAAACTGTGAAAT
+
DDDDDIIIHHIIIIIIIIIIIIIIIIHIIHIHHHIIIIIIIIHHHIIIII
@SRR7585268.2 SN363:854:H5VMFBCXX:2:1101:4701:2048/2
NAAGAACAAGCTGTATGAGCAGCATCTTGGAAAGTCCAACAACTTCCAGA
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585268.3 SN363:854:H5VMFBCXX:2:1101:5594:2101/2
CACCTAAAAAAAGATAATAACGTACTACAAAAACTCTACAAGATCGGAAG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH
@SRR7585268.4 SN363:854:H5VMFBCXX:2:1101:7631:2046/2
NAGCGGCCACAGAGCTGGAGAAAGAGGAAAGCCGCTGAGAATCTGAGAAG
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585268.5 SN363:854:H5VMFBCXX:2:1101:9001:2112/2
CTTCCCTCACTAATGCTACTACCACTAACCTGACTATCAAGCCCTAAAAA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Starting FASTQC command


Processing SRR7585268_1.fastq

Printing command:
fastqc --outdir SRR7585268_1.fastq

Analysis complete for SRR7585268_1.fastq

Processing SRR7585268_2.fastq

Printing command:
fastqc --outdir SRR7585268_2.fastq

Analysis complete for SRR7585268_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.0G
drwx------  3 varsha97 waxmanlab 4.0K Jul  3 11:59 .
drwxrwxrwt. 7 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 12:01 6_Liver_Basal_20_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.0G Jul  3 11:58 SRR7585268_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 1.0G Jul  3 11:59 SRR7585268_2.fastq
==========================================================
Finished on : Wed Jul  3 12:01:33 EDT 2019
0 hours, 3 minutes and 56 seconds elapsed.
==========================================================