-----------------------
Start of variable list:
-----------------------
Sample_ID:
2_Liver_Basal_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 11:57:37 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500897
Current job name : Step_02_2_Liver_Basal_3h
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500897.1.linga

Loading required modules...


List files in scratch directory:

total 661M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:00 .
drwxrwxrwt. 11 root     root      4.0K Jul  3 11:59 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:00 2_Liver_Basal_3h_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 298M Jul  3 11:59 SRR7585226_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 363M Jul  3 12:00 SRR7585226_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585226_1.fastq <==
@SRR7585226.1 SN363:854:H5VMFBCXX:1:1106:1507:2071/1
NCGCCGCAGACCCTGCCATCTATTTCAAAGAGCAGTTCTTGGACGGAGAT
+
#<DDDIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIHIIIIIII
@SRR7585226.2 SN363:854:H5VMFBCXX:1:1106:2006:2202/1
GACGCTACGCCGCGACGAGTAGGAGGGCCGCTGCGGTGAGCCTTGAAGCC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585226.3 SN363:854:H5VMFBCXX:1:1106:2231:2205/1
TAATAACGTACTACAAAAACTCTACATCTCAATACTAATCAGCTTACACG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585226.4 SN363:854:H5VMFBCXX:1:1106:2460:2059/1
NAGGTGAATGTCTGGTGAATGGCCCACTTTCACTGAGCACAGACAGCTAG
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH
@SRR7585226.5 SN363:854:H5VMFBCXX:1:1106:3331:2018/1
NGCTGTGGACCAGAGTGTGCTACTCCTGAAGCCCGAGTCTGAGCTCTCCC
+
#<<DDIHIIIHIIIIIIHIIIIIIGHIHGHHHIIHHIIIIIGCEHHHHHI

==> SRR7585226_2.fastq <==
@SRR7585226.1 SN363:854:H5VMFBCXX:1:1106:1507:2071/2
TACCACCAGTGTCTGGCCCTTATTGCTGAAGGGTTCGAATTTGGCGGACA
+
DBBD?HIHHHHHHEEHEHIEHFFH1CGHEHCHIFH?C<GCHI?G@CECD?
@SRR7585226.2 SN363:854:H5VMFBCXX:1:1106:2006:2202/2
TGGCGGCTCCACCCGGGCCCGCGCCCTAGGCTTCAAGGCTCACCGCAGCG
+
DDDD@HHDEHEHHI?HHHII?CCCHH<CGH@@G@CHCGG1DGHIEC/CC?
@SRR7585226.3 SN363:854:H5VMFBCXX:1:1106:2231:2205/2
TTTTTAGGGGGGTGGTTTTTTGTGTTTAGGGTTTTTTTTTTTGTTGTTTT
+
<<0<01111//////011<1//11111111111<1<///////111<111
@SRR7585226.4 SN363:854:H5VMFBCXX:1:1106:2460:2059/2
GCTCAGCGCTGTGTAATCTAGCCCTTGTTTGAACATTAATTGCTCTCATA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH
@SRR7585226.5 SN363:854:H5VMFBCXX:1:1106:3331:2018/2
TTGGGAAGAAATTTTTTTTTTGCATACCCGGGAGATTTTATATTCCGGAA
+
DD?B0<101<1<F1<DFH?///111<1<10////<1<1111111111<0<

Starting FASTQC command


Processing SRR7585226_1.fastq

Printing command:
fastqc --outdir SRR7585226_1.fastq

Analysis complete for SRR7585226_1.fastq

Processing SRR7585226_2.fastq

Printing command:
fastqc --outdir SRR7585226_2.fastq

Analysis complete for SRR7585226_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.6G
drwx------  3 varsha97 waxmanlab 4.0K Jul  3 12:01 .
drwxrwxrwt. 8 root     root      4.0K Jul  3 12:02 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 12:02 2_Liver_Basal_3h_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.3G Jul  3 11:59 SRR7585226_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 1.3G Jul  3 12:00 SRR7585226_2.fastq
==========================================================
Finished on : Wed Jul  3 12:03:00 EDT 2019
0 hours, 5 minutes and 23 seconds elapsed.
==========================================================