-----------------------
Start of variable list:
-----------------------
Sample_ID:
4_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 11:57:37 EDT 2019
Running on node : scc-kb1
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500907
Current job name : Step_02_4_Liver_Low_20
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500907.1.linga

Loading required modules...


List files in scratch directory:

total 580M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 11:59 .
drwxrwxrwt. 10 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 11:59 4_Liver_Low_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 264M Jul  3 11:58 SRR7585245_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 317M Jul  3 11:59 SRR7585245_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585245_1.fastq <==
@SRR7585245.1 SN363:854:H5VMFBCXX:2:1101:2655:2163/1
CTTTTGTTAACGTTGTTAGGCTGTCTGTGTTTGACTCTTTGGGTGACAGT
+
@B@DAGHEHHII<CGIIHHIG?HIIHIGHEHFIIH?@CCFFGHHCHFHHC
@SRR7585245.2 SN363:854:H5VMFBCXX:2:1101:3839:2139/1
AATTAGTGACGCGCATGAATGGATGAACGAGATTCCCACTGTCCCTACCT
+
DDDDDHIIIIIIIIIIIEHIIIIIIIIIIIIHIIIIIIHHIIIIHIIEHH
@SRR7585245.3 SN363:854:H5VMFBCXX:2:1101:4346:2056/1
NCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAAC
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIII
@SRR7585245.4 SN363:854:H5VMFBCXX:2:1101:5506:2065/1
NAGAACTTTCCAGAACCTTAGATCATGTGTTCTTGGTGCTGCCAAACCAC
+
#<DDBHHIIIIIIIIIIIIIIHIIIIIHEHIHIIHGGCHHIIIIIIIIII
@SRR7585245.5 SN363:854:H5VMFBCXX:2:1101:5627:2100/1
CATAAGGCCGTGCTGACCATCGATGAGACAGGAACAGAAGCTGCAGCAGC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

==> SRR7585245_2.fastq <==
@SRR7585245.1 SN363:854:H5VMFBCXX:2:1101:2655:2163/2
AAAAAACAAAAGCAGCCAAGTCGCAGCCTACAAAGAACAGCAACTGTCAC
+
DDDDDHEHHIEHEHI1F@HHEHHHHHIIHGHIIHHHIIIGHIGFH1D1C1
@SRR7585245.2 SN363:854:H5VMFBCXX:2:1101:3839:2139/2
TGTCTCTTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTC
+
DDDDDIIIIIIHIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIGIH
@SRR7585245.3 SN363:854:H5VMFBCXX:2:1101:4346:2056/2
TGGTTTTTTTGGGCTGGGGGGGGGTCAATTTTTAATACCAGGGGGGGGGG
+
<00<<C11/<//01100<C/////<<111<<F1111111111<</EHHH<
@SRR7585245.4 SN363:854:H5VMFBCXX:2:1101:5506:2065/2
TGGGGTGCTCCAGGCATAGAAGCTCTCCTGGTACTGGATGTTGTACTTCT
+
DDDDB<EHGEHHCH?FCHHHHIIHEHCHHHIIGHIII@GHHIIFEGGHCG
@SRR7585245.5 SN363:854:H5VMFBCXX:2:1101:5627:2100/2
TGAGAGTGTTCTTCAAATATTATGAAAAGGAAAGGGCGGTTGAAGTGCAA
+
DD@BBGGEGHEHHEGHICGGH@CC@HIIEH?HHEHICHI/CC<F@CCEGH

Starting FASTQC command


Processing SRR7585245_1.fastq

Printing command:
fastqc --outdir SRR7585245_1.fastq

Analysis complete for SRR7585245_1.fastq

Processing SRR7585245_2.fastq

Printing command:
fastqc --outdir SRR7585245_2.fastq

Analysis complete for SRR7585245_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.4G
drwx------  3 varsha97 waxmanlab 4.0K Jul  3 11:59 .
drwxrwxrwt. 8 root     root      4.0K Jul  3 12:00 ..
drwxr-xr-x  2 varsha97 waxmanlab 4.0K Jul  3 12:01 4_Liver_Low_20_FASTQC
-rw-r--r--  1 varsha97 waxmanlab 1.2G Jul  3 11:58 SRR7585245_1.fastq
-rw-r--r--  1 varsha97 waxmanlab 1.2G Jul  3 11:59 SRR7585245_2.fastq
==========================================================
Finished on : Wed Jul  3 12:01:26 EDT 2019
0 hours, 3 minutes and 49 seconds elapsed.
==========================================================