-----------------------
Start of variable list:
-----------------------
Sample_ID:
Nudt7_1365
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Scripts/00_Setup_Pipeline
BU_User:
varsha97
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE125237
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Jun 24 15:50:39 EDT 2019
Running on node : scc-ka3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Scripts/02_FASTQC
Current job ID : 7055552
Current job name : Step_02_Nudt7_1365
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055552.1.linga

Loading required modules...


List files in scratch directory:

total 1.3G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 15:52 .
drwxrwxrwt. 12 root     root      4.0K Jun 24 15:50 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 15:52 Nudt7_1365_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 646M Jun 24 15:51 SRR8450740_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 662M Jun 24 15:52 SRR8450740_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8450740_1.fastq <==
@SRR8450740.1 1/1
TCGTAGATGGCGAACAGGAAGGGGCTGCTCAGGGTCACATCCAGTGCCTCC
+
BBBFFFBFFFFFFIFFIIBFFIIIIFFIIIIIFIFFFFFFFFFFFI<FFII
@SRR8450740.2 2/1
CCTCGATTGGCCTCTCTGGTTACCCCACTGCCCTGGCACTTCCCAGAAAAC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIII
@SRR8450740.3 3/1
NGCCACTCCGGATTCGGGGATCTGAACCCGACTCCCTTTCGATCGGCCGAG
+
#0<FFFFFFFFFFIIIIIIIIIIFI<<<<BFFIIIFIIIIFFIIIFFFFFF
@SRR8450740.4 4/1
GTCTTTATATAAAAACAACTAAAGGTAAGCTACTTCAATAACATTTAACTA
+
BBBFFFFFFFFFFIIIFIIIIFFFFFFFFFBFFFIFFFFFFFFFFIIIFII
@SRR8450740.5 5/1
CCTTGGGTTCCCTTCTCCACAAAATCATTAATCACTTTCTTGGCCTCCTCT
+
BBBFFFFFFFFFFIIIIIIIIIIIIIFIIIIIIIIIIIIFIFFIIIIIIII

==> SRR8450740_2.fastq <==
@SRR8450740.1 1/2
CGTCTGTCCAGCAGCCTGGCTCACCGGAGGCACTGGATGTGACCCTGAGCA
+
BBBFFFFFBFFFFIFIFIIIIIIIIIBBFFIFFFFIFIIIIFFFIIFFIII
@SRR8450740.2 2/2
GCTCATTTGACTTGGCTTGTCCCTTGGGTGTTGACTGAAATGTCCCAGGAG
+
BBBFFFFFFFFFFIIIIIIFIIIIIIIIFFIFFFFIFFIFFIFIIIFFIFF
@SRR8450740.3 3/2
CATGTGAACAGCAGTTGAACATGGGTCAGTCGGTCCTGAGAGATGGGCGAG
+
BBBFFFFFFFFFFIIIIIIIIIFIIFIIIIIIIIFIBFIIIFFBFFIIIII
@SRR8450740.4 4/2
CAAGCTCATAGACGAAACCCTATCTGTTTCAGTTAGTTAAATGTTATTGAA
+
BBBFFFFFFFFFFIFIIFFFFFIIFIFFIIIIFIFIFFIIFFIIIFIIF<F
@SRR8450740.5 5/2
GACAGTGAGCTGCAGCTGAGCACAGGCAATGGCCTCTTTGTCAACAATGAC
+
BBBFFFFFFFFFFFFIIIIIIIIIIIIFIFIIIIIIIIIIIIIIFFIFIFF

Starting FASTQC command


Processing SRR8450740_1.fastq

Printing command:
fastqc --outdir SRR8450740_1.fastq

Analysis complete for SRR8450740_1.fastq

Processing SRR8450740_2.fastq

Printing command:
fastqc --outdir SRR8450740_2.fastq

Analysis complete for SRR8450740_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 5.2G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 15:53 .
drwxrwxrwt. 17 root     root      4.0K Jun 24 16:05 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 15:59 Nudt7_1365_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 2.6G Jun 24 15:51 SRR8450740_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 2.6G Jun 24 15:52 SRR8450740_2.fastq
==========================================================
Finished on : Mon Jun 24 16:09:21 EDT 2019
0 hours, 18 minutes and 48 seconds elapsed.
==========================================================