-----------------------
Start of variable list:
-----------------------
Sample_ID:
2_Liver_High_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-kb2
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500899
Current job name : Step_02_2_Liver_High_3h
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500899.1.linga

Loading required modules...


List files in scratch directory:

total 711M
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 12:00 2_Liver_High_3h_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 331M Jul  3 11:59 SRR7585228_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 380M Jul  3 12:00 SRR7585228_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585228_1.fastq <==
@SRR7585228.1 SN363:854:H5VMFBCXX:1:1106:2006:2012/1
NAAGATCAGAGACTGCCTTGTGTGGAAGACTATCTGTCTGCAATCCTGAA
+
#<DDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585228.2 SN363:854:H5VMFBCXX:1:1106:2993:2227/1
CATGACTCTGAGATAGCCTCGGGAGCTGCATTTAGAAACTCTATGCATTG
+
DDDDDIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIH
@SRR7585228.3 SN363:854:H5VMFBCXX:1:1106:2889:2235/1
TTATGATCCGAATGAAAAGAGTAAACATAAGTTCATGGTACAGACAATTT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585228.4 SN363:854:H5VMFBCXX:1:1106:3771:2142/1
AGGCTGTCTTGGAGCTCATTATACAACCCAGGCTGGCCTCAAACTGACTG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIII
@SRR7585228.5 SN363:854:H5VMFBCXX:1:1106:4113:2134/1
AGATTGAGAAGGTCGTTCTCCACCCCAACCACTCCGTGGTGGATATCGGG
+
DDDDBHIIHHHIIIHIIIIHIIHHHIIIIHHHIIHHHIIIIIIIIIHHHH

==> SRR7585228_2.fastq <==
@SRR7585228.1 SN363:854:H5VMFBCXX:1:1106:2006:2012/2
GAGCAGAGAAGCATGGCCGCCTTTCCACCAGGGATCCACTACAGCACTTG
+
DDDDDIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585228.2 SN363:854:H5VMFBCXX:1:1106:2993:2227/2
AGACAGACCTCCAGGTCAAACTTGCCGTGGGATCTTCAAGCAAGGGGCCT
+
DDDDDIIIIIIIIIIHIIIIIIIIIIIIIIIGIIIIIIIIIIIIHIHIII
@SRR7585228.3 SN363:854:H5VMFBCXX:1:1106:2889:2235/2
ATTTTCATTCGGCATTTCAAACACACATCTCAATTTAGAATCCATTAATT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585228.4 SN363:854:H5VMFBCXX:1:1106:3771:2142/2
TTGTATCTCCCGACTTTTGGGGGGGGGGGGGGGGGGGTACAAGCAGGTTT
+
<000<11111</0//<11</<FH/C<CDD//</<D<//011111<11<<1
@SRR7585228.5 SN363:854:H5VMFBCXX:1:1106:4113:2134/2
GGTGCTATGTAGTCTTTGGAAGGCAGGCAGATAGGCATGACTCTCTCGGT
+
DDDDAHIIIIIIHHHIIIIIIIIIIIHGIIIIIHIIIIGHIIHIIIIIIH

Starting FASTQC command


Processing SRR7585228_1.fastq

Printing command:
fastqc --outdir SRR7585228_1.fastq

Analysis complete for SRR7585228_1.fastq

Processing SRR7585228_2.fastq

Printing command:
fastqc --outdir SRR7585228_2.fastq

Analysis complete for SRR7585228_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 2.9G
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:01 .
drwxrwxrwt. 11 root     root      4.0K Jul  3 12:03 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:03 2_Liver_High_3h_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.5G Jul  3 11:59 SRR7585228_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 1.5G Jul  3 12:00 SRR7585228_2.fastq
==========================================================
Finished on : Wed Jul  3 12:03:48 EDT 2019
0 hours, 6 minutes and 12 seconds elapsed.
==========================================================