-----------------------
Start of variable list:
-----------------------
Sample_ID:
2_Liver_Basal_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-kb6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/Scripts/02_FASTQC
Current job ID : 7500894
Current job name : Step_02_2_Liver_Basal_20
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7500894.1.linga

Loading required modules...


List files in scratch directory:

total 450M
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:00 .
drwxrwxrwt. 15 root     root      4.0K Jul  3 11:57 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:00 2_Liver_Basal_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 244M Jul  3 11:59 SRR7585220_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 206M Jul  3 12:00 SRR7585220_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR7585220_1.fastq <==
@SRR7585220.1 SN363:854:H5VMFBCXX:2:1101:1628:2118/1
AGCCAGCAAAAAGGGCACCGCGATCGTGCCACTGAAACACGTCAGGTAGT
+
@D?DBFGGHIIIIHHHIIHIHIHIHIIHIHHHIIIIHHIHIHIIIHHHHH
@SRR7585220.2 SN363:854:H5VMFBCXX:2:1101:1865:2174/1
GCCACTAGGCAGCTTAACTCACCCGGGACTTGGAATATGGCTGCACAGCG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGEHIIIH
@SRR7585220.3 SN363:854:H5VMFBCXX:2:1101:1874:2203/1
TCTCTACCCCAATCTCCTGCCGACAAAAAGTTCTGGCAAACTTATTTCTT
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585220.4 SN363:854:H5VMFBCXX:2:1101:3776:2051/1
TCTTGATTCTTCATTTAAACCCAATATTTCAGCGTCTCTTAGAACTGGTC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH
@SRR7585220.5 SN363:854:H5VMFBCXX:2:1101:4056:2085/1
TGTCTATATCGATAATGGCAGAATATTCAGTCAGCGTCACACATCTCCAG
+
DD@DBHHEEEHHHHHEHIHEFGH@F<GE@EHHHHFCGEHHECCEEE@H?@

==> SRR7585220_2.fastq <==
@SRR7585220.1 SN363:854:H5VMFBCXX:2:1101:1628:2118/2
ATCCCCAGAGGTCGGATATGATCTACACTATAGAAGATGTTCCTCCCTGG
+
BDDDDHHHHEHHIIIHCH<<CHHHHIIIIIIIIHEHHHHIHIHIHEEEGH
@SRR7585220.2 SN363:854:H5VMFBCXX:2:1101:1865:2174/2
AAAGCGCGGACTAATTTAGAGCCTCTGTAACACAGCACTTAGGAGATTGC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIHI
@SRR7585220.3 SN363:854:H5VMFBCXX:2:1101:1874:2203/2
AAAATAAGTAGGACATGTTCTTGGACTTAATCTATTAAAAGTTAGCTCTC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585220.4 SN363:854:H5VMFBCXX:2:1101:3776:2051/2
NTATTAAAAATAAGCGTTCATTATAAATTGTACTTGAAATATATGACATT
+
#<DDDIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIII
@SRR7585220.5 SN363:854:H5VMFBCXX:2:1101:4056:2085/2
TCCTGGACCAAAGTGGCACCAAGATCTACGTGTGGAAAGGCAAAGGAGCC
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Starting FASTQC command


Processing SRR7585220_1.fastq

Printing command:
fastqc --outdir SRR7585220_1.fastq

Analysis complete for SRR7585220_1.fastq

Processing SRR7585220_2.fastq

Printing command:
fastqc --outdir SRR7585220_2.fastq

Analysis complete for SRR7585220_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.9G
drwx------   3 varsha97 waxmanlab 4.0K Jul  3 12:01 .
drwxrwxrwt. 14 root     root      4.0K Jul  3 12:03 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jul  3 12:03 2_Liver_Basal_20_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 929M Jul  3 11:59 SRR7585220_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 929M Jul  3 12:00 SRR7585220_2.fastq
==========================================================
Finished on : Wed Jul  3 12:03:43 EDT 2019
0 hours, 6 minutes and 6 seconds elapsed.
==========================================================