-----------------------
Start of variable list:
-----------------------
Sample_ID:
Nudt7_1359
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 16:17:19 EDT 2019
Running on node : scc-ka5
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Scripts/02_FASTQC
Current job ID : 7055553
Current job name : Step_02_Nudt7_1359
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/7055553.1.linga

Loading required modules...


List files in scratch directory:

total 1.2G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:32 .
drwxrwxrwt. 18 root     root      4.0K Jun 24 16:15 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:32 Nudt7_1359_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 563M Jun 24 16:22 SRR8450741_1.fastq.gz
-rw-r--r--   1 varsha97 waxmanlab 574M Jun 24 16:32 SRR8450741_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR8450741_1.fastq <==
@SRR8450741.1 1/1
GCCAGGTAACCACCAATCACCTCAATCTCGTGCACAGTGGGGTATCGTTTC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIFFFIIFFIIIFFIF
@SRR8450741.2 2/1
NCTGGACATCTGCACTGCCACCCCCTAACCAGAGTTACAAGAGCTTCTTAG
+
#0<FFFFFFFFFFIIIFI<FFFFIIIIIIIIIFFFIIIIIIIIIIIIIIII
@SRR8450741.3 3/1
TTTGTTTCTTAATCTGCTTCTCCTTCTCTGGAAGTGTGCAGATATCAGAGT
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIFFFFIIIIIIIIIIFIIFIB
@SRR8450741.4 4/1
ACCCCTGGAAAAAGCAGAGCCGGAGACGAAGAGGAGGAGGAGAAAGGCTAC
+
<BBBFFFFFFBBFIFIF<FBFBB7FFFFF0BFBF''7<7<7<BBFB7707B
@SRR8450741.5 5/1
CTCATGATGTGGGCTGGGGAGAAGAAGTGGGTGCCAATCACCAGCTGGGGG
+
BBBFFFFFFFFFFIIIIIIIIIIIFIIBFFFBFFFFBFIFIIBFFIIIIII

==> SRR8450741_2.fastq <==
@SRR8450741.1 1/2
CTTAAGTCAGACCAATGGTCAGTCCCAGCAAGGGGCAGAGGAACAGGATGC
+
BB<FFFFFFFFFFIIFIFFIIIIIIIIIIIIIIIFFFIIIIIIIIIIIIII
@SRR8450741.2 2/2
TAAAAACATAAAAGCATTCTTTTGATATCTCCCAGTAGAAAGCCATGAACA
+
BBBFFBFFFFFFFIIBIIIIFIIIIIFIIIFIIIIIIFIIIFIFIFIFFIF
@SRR8450741.3 3/2
CTGCTCTGACAGTTGATGAAACATATGTCCCCAAAGAGTTTAAAGCTGAGA
+
BBBFFFFFFFFFFIIIIIIFIIFIFIIIIIIIIIIIFIIIIFFIIIIIIII
@SRR8450741.4 4/2
CTAGCCTCTGGCAAAATGAAGTGGGTAACCTTTCTCCTCCTCCTCTTCGTC
+
BBBFFFFFBFFFBFIIFIFIBBFFFBFFBBF<B0<BBFFFBFIIIFB<FFF
@SRR8450741.5 5/2
GGTTGCTGTAGAGTCAGACCCAAAGCAGCTAGATACTGCAAAGAAGATAAT
+
BBBFFFFFFFFFFFIIFIIIFIIIIFFIIIIIFIIIIFIIBFIFFIFIFII

Starting FASTQC command


Processing SRR8450741_1.fastq

Printing command:
fastqc --outdir SRR8450741_1.fastq

Analysis complete for SRR8450741_1.fastq

Processing SRR8450741_2.fastq

Printing command:
fastqc --outdir SRR8450741_2.fastq

Analysis complete for SRR8450741_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 4.5G
drwx------   3 varsha97 waxmanlab 4.0K Jun 24 16:34 .
drwxrwxrwt. 15 root     root      4.0K Jun 24 16:40 ..
drwxr-xr-x   2 varsha97 waxmanlab 4.0K Jun 24 16:41 Nudt7_1359_FASTQC
-rw-r--r--   1 varsha97 waxmanlab 2.3G Jun 24 16:22 SRR8450741_1.fastq
-rw-r--r--   1 varsha97 waxmanlab 2.3G Jun 24 16:32 SRR8450741_2.fastq
==========================================================
Finished on : Mon Jun 24 16:41:41 EDT 2019
0 hours, 24 minutes and 22 seconds elapsed.
==========================================================