-----------------------
Start of variable list:
-----------------------
Sample_ID:
Old-hMANF-HTV4
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE123115
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Jun 28 11:09:02 EDT 2019
Running on node : scc-kb5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Scripts/02_FASTQC
Current job ID : 7268846
Current job name : Step_02_Old-hMANF-HTV4
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7268846.1.linga

Loading required modules...


List files in scratch directory:

total 3.4G
drwx------   3 varsha97 waxmanlab 4.0K Jun 28 11:11 .
drwxrwxrwt. 17 root     root      4.0K Jun 28 11:09 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 28 11:11 Old-hMANF-HTV4_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 1.6G Jun 28 11:10 SRR8261784_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 1.8G Jun 28 11:11 SRR8261784_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261784_1.fastq <==
@SRR8261784.1 1/1
NCCAGCCAAAAAGTAACTCTTCTTTGCATTCTGCATAGCCTTGTGGGGCTGGGCAGCAGGAACACATCTGGTATTCTGTATTCCAAAAGTACCTGAAATCAAGATCAGACCAACACCTGCATCCTCGGCTCTCTCGGGCCAATGAGATCG
+
#AAAFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJFJJJJJ<FJJJFFJJFJJJJJJFFFJJFJJAF
@SRR8261784.2 2/1
NGGGCACTTCAGGTTCTCTGTTCTTGTCCTCAAGTTGTCTTTTCTATATCACAAAGAGACAGAATAGCTCAACTAATAATTTTGCCAAGCCTACATGGCTGTTTTTTTCTTCCTCTGATATTCCTAGAGCTGCCAAAGGGATTGGTTCTA
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFAJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFJFFJJJJFJJF
@SRR8261784.3 3/1
NAGCAATATAGAGATTCCTCTGAGCACGGAAAAGCTTCATGTGGAAGTGCTCCATGGCACCTGGATTGTTCTGGAGGTTCACCTTTTCTGTCACATCATCGTATTTCAGGATCTCTCGTACAGCATCAATAACCAACAGATCGGAAGAGC
+
#AAAAFJFJJJ-FFJJFFJJJJJJJJJJJJJJJFF<<FAJFJFJJAJJJJJJFJFJJJFJFFJJFJJJJFF<<A<AA-AAAJJJFJA-AA<AFAJJFFJAAAJJJJJFF7JJJJFJFFF<<AAA-7FJJFA<A-FAA-FFFF-F-<FFFF
@SRR8261784.4 4/1
NTGGACTTGACCTGCCAGAGATCTAGGCCCAGTACAGCAAAACTATCATAGGCATAGATATTTGCATCGGGGGAGTATTCAGGGTTGTCAATTTCTGGGTGTATCCAGGTACCCTTGTAATCTGGGTTGTCAATTTGACGTGGTTTCCAC
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@SRR8261784.5 5/1
NCAGTATAAAGCTGATTCCAGTTCTTCTCATTAAATGTTTGGAACCAAAAGTCAAAACACAGCATATAGATGACATTTCTCACCCTCTCCATGAAAGTCATCCTGTCACTCAATTCTGACATAACAACAGGCACATAGGAAGGAGGCAGT
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJFJJJJJFJJJJJJJJJJJJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJF

==> SRR8261784_2.fastq <==
@SRR8261784.1 1/2
NATTGGCCCGAGAGAGCCGAGGATGCAGGTGTTGGTCTGATCTTGATTTCAGGTACTTTTGGAATACAGAATACCAGATGTGTTCCTGCTGCCCAGCCCCACAAGGCTATGCAGAATGCAAAGAAGAGTTACTTTTTGGCTGGGAGATCG
+
#AAFFJJJJJJJFJJJJJJJFJJJJJJJFFJJJJFFFJJJJFJJJJJJJAJFJ7AJJJJJJJJJJJJJJJF<AJJJAAJFAJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJJJJFAFJJJJJJJJJ<FJJJJJJAFJJJJJ<JA
@SRR8261784.2 2/2
NTTTCTCTCAAAGGAGGAAATATGCGTGACATCCATTTGTCAGACCTGTAATGGCCTGACGCCACGAGGGTTTACCCCTACGTGAGTAGATAAAATTTGACAACAATCTAAAGGCATTATTAAGTAATCAGAATCATTTCTAGTAGAACC
+
#AAFFJFFJJFFFJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFFFJJFAAFJFFJJJJJJJJFJJJFJJJJJJJAJJFJJJJ
@SRR8261784.3 3/2
NTTGGTTATTGATGCTGTACGAGAGATCCTGAAATACGATGATGTGACAGAAAAGGTGAACCTCCAGAACAATCCAGGTGCCATGGAGCACTTCCACATGAAGCTTTTCCGTGCTCAGAGGAATCTCTATATTGCTGAGATCGGAAGAGC
+
#AAFFFJJJJJAJJJJJJJJFJ<JJJFJJJFF<F<FJJFJJJFJJJJAFJFJJ<<AFJFAFJJFJFJJJJJFJJJJFJJFJJJJJFJJJJJJJJFJJJJFJJJJFJJJFFFJJJJJJJF7AJJJFFJFJJJFJFJAFJ<AFFFFJA-FAF
@SRR8261784.4 4/2
NGAGTGGGAACCACCAGTGATTCAAAATCCTGAATACAAGGGCGAGTGGAAACCACGTCAAATTGACAACCCAGATTACAAGGGTACCTGGATACACCCAGAAATTGACAACCCTGAATACTCCCCCGATGCAAATATCTATGCCTATGA
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ
@SRR8261784.5 5/2
NTCCGCTTCTTTCCTGGCTCCACTTATGAGAAGTACAGTGGGGGACTCCCACTGCCTCCTTCCTATGTGCCTGTTGTTATGTCAGAATTGAGTGACAGGATGACTTTCATGGAGAGGGTGAGAAATGTCATCTATATGCTGTGTTTTGAC
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJFJJJJJJJJJJJJJJJJJJJJJJJFJJJFFJJFJJJJJJJAFJJJJJJFJJJFAJJJJJFFAAFJJJFFF

Starting FASTQC command


Processing SRR8261784_1.fastq

Printing command:
fastqc --outdir SRR8261784_1.fastq

Analysis complete for SRR8261784_1.fastq

Processing SRR8261784_2.fastq

Printing command:
fastqc --outdir SRR8261784_2.fastq

Analysis complete for SRR8261784_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 15G
drwx------   3 varsha97 waxmanlab 4.0K Jun 28 11:14 .
drwxrwxrwt. 15 root     root      4.0K Jun 28 11:23 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 28 11:24 Old-hMANF-HTV4_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 7.1G Jun 28 11:10 SRR8261784_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 7.1G Jun 28 11:11 SRR8261784_2.fastq
==========================================================
Finished on : Fri Jun 28 11:24:07 EDT 2019
0 hours, 15 minutes and 5 seconds elapsed.
==========================================================