-----------------------
Start of variable list:
-----------------------
Sample_ID:
Yg_WT1
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE123117
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 15:49:00 EDT 2019
Running on node : scc-ka6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Scripts/02_FASTQC
Current job ID : 7055526
Current job name : Step_02_Yg_WT1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055526.1.linga

Loading required modules...


List files in scratch directory:

total 4.5G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 15:54 .
drwxrwxrwt. 15 root     root      4.0K Jun 24 15:48 ..
-rw-r--r--   1 varsha97 waxmanlab 2.1G Jun 24 15:51 SRR8261613_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 2.4G Jun 24 15:54 SRR8261613_2.fastq.gz
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 15:54 Yg_WT1_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8261613_1.fastq <==
@SRR8261613.1 1/1
NCTCCTTTGGGGTTGCCTGTAGTTCCACTTGTGAAACAAATTATCGCAAGATCTTCGGGTTCTGGAGGCTTGGGCTTCACTCTGTTCACTCTTCCAAGGTCCTCCAGAGCTTTGAGGCTGAGATCGGAAGAGCACACGTCTGAACTCCAG
+
#AAFFAAFFJJJJAJJJJ<JJFFJJJJJJJFAAFJJJJJJJ<JJJFJJJJFFJJFJJJJJJJJFJJJJJJF-FFJAFJJJJJJJJJJJJJ<FJJJJJJ7JJJJJJJFJ-AFFJ<J-7AFF<FJF-AJFAJJJJFAAAFAJJJFA<JJJJF
@SRR8261613.2 2/1
NCTAGACTAGAGCAGGACAGGGAAAGAATGGGTCCTGGGTGAGGCCGTGCAGCACATCTGACCCTCCCGTCCTGCTGCAAACCCAGTGAACAGCTGTGGCCTCAGATGAGCTGGGGCTGGGTTCTTGCCCACACCAAGTGGCCCTGCTGT
+
#<AFFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJJJFJJFJJ<AJJFJJJJJJJJJJJJJFJ<FFFJFJJJJJJJJJJJJJJJJ<FJJJJJJ
@SRR8261613.3 3/1
NAGGGTGTGTGTTGTGAATGATAAAATTATGAGGTTTAGGGTTCCTACATGGTTTTGGATTAAGATGAGGGCAATTAGCAGTGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCTCGTATGCCGTCTTCTGC
+
#AAFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJAJJJJJFFJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFFJJFJJJJJJJJJJJJJJ
@SRR8261613.4 4/1
NGGGTCTTCTCATGCAGCAGACACACACGGTTCAGGATTGCAGACAGATAGTCTTCCACACAAGGCAGTCTCTGATCTTCAGGAAGTGTACAACACTTGGTGCCCACTCTTCCTAGGTTTCTTGCAGCCTCCACGAGAGTTGGGAGATCG
+
#AAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFJAAFJJJJJJJJ
@SRR8261613.5 5/1
NCCATCTCAGGGTGAGGGGCTCAGGCAGCCCCTCATGGTACACATGGCATGTGTAATTCTGCTCCTTCCCAAGAGGCACCACCACAGATGCCCACTTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCTCGTA
+
#AAFFJJJJJJJJJJJJA<FAJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFJ<F<AFJJJJFJAAAJAJJJJJJJFAJJJF7FJFJJJJJ-7F77JFJJJJ<7-FFJJJJJJJ<FJAJJFJFJFFFFF7FFJJJJJJJJAFF-7AAFJA

==> SRR8261613_2.fastq <==
@SRR8261613.1 1/2
NAGACTCAAAGCTATGGAGGACCTTGGAAGAGTGAACAGAGTGAAGCCCAAGCCTCCAGCACCCGAAGATCTCGCGATAAATTGTTTCACAAGTGGAACTACAGGCAACCCCAAAGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAG
+
#A--<-A7<7----<<-A--FA7--7--7A<---<FAAFFF-7FA-<FJ7FJ-<-77A<-FAF<AFA<7--7-77--7F7-7AJ7F-FF-FF-<-<-AA-FFF-F)-A-<))77A<7-)-)7F7FA)<-)7-<A)))7A-A---7<A7<-
@SRR8261613.2 2/2
NTTATCTGTGTGGCTTCCTCTTTCTGTTCTAATACTGGTAATCAGTGGAAACCCTCTACAGCTAATGACCTCGGCTCAGTGTCAACAGCAGGGCCACTTGGTGTGGGCAAGAACCCAGCCCCAGCTCATCTGAGGCCACAGCTGTTCACT
+
#A7--<FF7J7-77---7F7FJ7J7<JF-FFAFFJ-7<F7<AJ<FAAFF<AJF-A-77-F7F7-AFF-FA7-F<JJF7A<--7<FFFFA<-F-7-AAAFFAJAFJ7JJ<<<AFJF<F<A)-A-F<AJJAAJJAAJJF))7A<FJ-77A--
@SRR8261613.3 3/2
NTTCCACTGCTAATTGCCCTCATCTTAATCCAAAACCATGTAGGAACCCTAAACCTCATAATTTTATCATTCACAACACACACCCTAGGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTATAGTGTAGATCTCGGTGGTCGCCG
+
#AAFFAJJJJJJJJFJJFJFJFJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJFJJJJFJJJJFJF<JJJJJJJFJFFJJJJJJJJJJJJJJJFJJJJJJJJFJFJJJJJJJJAF<J<JJJJFJ<FFJJJ<<F<F<A<7<FJJJJJJJJF
@SRR8261613.4 4/2
NCCAACTCTCGTGGAGGCTGCAAGAAACCTAGGAAGAGTGGGCACCAAGTGTTGTACACTTCCTGAAGATCAGAGACTGCCTTGTGTGGAAGACTATCTGTCTGCAATCCTGAACCGTGTGTGTCTGCTGCATGAGAAGACCCCAGATCG
+
#AAFFJJJJJJJJJJJJJJJJJJJFJJJJJFFFJJJJJJJJJJJJJJFAJJJJJJJJJJJJJJJJJJFJJJJJFJJFJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJ<FFFJJJJJJJJJJJFJJJ<JJJJ
@SRR8261613.5 5/2
NAGAAGTGGGCATCTGTGGTGGTGCCTCTTGGGAAGGAGCAGAATTACACATGCCATGTGTACCATGAGGGGCTGCCTGAGCCCCTCACCCTGAGATGGGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTATAGTGTAGATC
+
#AAAFAFJ7FJJA<JJ7F-FFJ<JJJJJJJJJJFJJJJFFJJJFJJJJJJ7A7JJFFJJFJFJ7JJF7AJ<JFJF-7FJJJJ<AFFAJJ-FJFFJAFFJJJJ7-FJ<-FJFJJF7<--<<JJJJAF<<7F<JFJA-7<AJA<<-FFAFF-

Starting FASTQC command


Processing SRR8261613_1.fastq

Printing command:
fastqc --outdir SRR8261613_1.fastq

Analysis complete for SRR8261613_1.fastq

Processing SRR8261613_2.fastq

Printing command:
fastqc --outdir SRR8261613_2.fastq

Analysis complete for SRR8261613_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 20G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 15:58 .
drwxrwxrwt. 15 root     root      4.0K Jun 24 16:02 ..
-rw-r--r--   1 varsha97 waxmanlab 9.8G Jun 24 15:51 SRR8261613_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 9.8G Jun 24 15:54 SRR8261613_2.fastq
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:13 Yg_WT1_FASTQC
==========================================================
Finished on : Mon Jun 24 16:13:47 EDT 2019
0 hours, 24 minutes and 47 seconds elapsed.
==========================================================