-----------------------
Start of variable list:
-----------------------
Sample_ID:
KI11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/GSE96650_LxRKo_ENV
OUTPUT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Apr 29 14:25:27 EDT 2019
Running on node : scc-ka3
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/GSE96650_LxRKo/Scripts/02_FASTQC
Current job ID : 5758564
Current job name : Step_02_KI11
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5758564.1.linga

Loading required modules...


List files in scratch directory:

total 303M
drwx------   3 kkarri waxmanlab 4.0K Apr 29 14:25 .
drwxrwxrwt. 94 root   root      108K Apr 29 14:25 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 14:25 KI11_FASTQC
-rw-r--r--   1 kkarri waxmanlab 150M Apr 29 14:25 SRR5345554_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 154M Apr 29 14:25 SRR5345554_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR5345554_1.fastq <==
@SRR5345554.1 1/1
TTCTGGGGGTTGCTGACGACAGCCGTGGTGCTGTAGGAGTATG
+
AAAA6EEEEEEEEEEEEE/EEEEEAAAEEEEEEE6EEEEEEEE
@SRR5345554.2 2/1
CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATGGGGTTTTTTT
+
AAAAAEEEEEEEEEEEEEEEEEEEEEEE/////////</EE/E
@SRR5345554.3 3/1
CTTCATCTTGAACTTGGCAGGATCTTCAGTGTCTGTGAAAGTG
+
AAAAAEEEEEEAEEEEEEEEAAEEEEEEAEEEAEEEEEE/EAE
@SRR5345554.4 4/1
AAATGTTTTACCACACTGTTTACATTCATAGGGTTTTTCATC
+
AAAAAEEEEAEAEAEEEEEEEAE/EEEEEAE/AEEE/A///A
@SRR5345554.5 5/1
TTCAGCATCTCCTCGCTCTTCCGGGGGAAGTTCTTCCCAAAGC
+
AAA/AAA/E/EEE6EAE/EEA/EEEAEEEEEEEAEEEAEE/EA

==> SRR5345554_2.fastq <==
@SRR5345554.1 1/2
GGTTGCTTTGCCATCGCCACTACACCATCGCAGCCCTGCTC
+
AAAAAEEEE/EE/EEEEEEAEEEAE<<EA/<EEEAEEEEEE
@SRR5345554.2 2/2
ATAAAGGATGCTAAATTCAACCTACAGTCACAAAACAGCAAA
+
///////A//////////AA/////<////</////A/////
@SRR5345554.3 3/2
AGCGCCACAGCCAAGGGACGAGTCCGTCTTCTGAGCAACTGGG
+
AAAAAEEEEEAEEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE
@SRR5345554.4 4/2
GCTATCCATGTAAATCCGCATGCGATCAGTGTGGCCAGTCCTT
+
6AAAAEEEEA/E<EEEEEEEE/EAEEEEEE6EEEEEEEEEEEE
@SRR5345554.5 5/2
CGTCAGCAAGCTTCAGAAGGCGATGGCAGCGGTTGGCCACTTC
+
AAAAAEEEE/E/EEAE//E/EE/<EAEEE/EEAEEEEE/EA/E

Starting FASTQC command


Processing SRR5345554_1.fastq

Printing command:
fastqc --outdir SRR5345554_1.fastq

Analysis complete for SRR5345554_1.fastq

Processing SRR5345554_2.fastq

Printing command:
fastqc --outdir SRR5345554_2.fastq

Analysis complete for SRR5345554_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Apr 29 14:26 .
drwxrwxrwt. 81 root   root      108K Apr 29 14:27 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Apr 29 14:27 KI11_FASTQC
-rw-r--r--   1 kkarri waxmanlab 594M Apr 29 14:25 SRR5345554_1.fastq
-rw-r--r--   1 kkarri waxmanlab 594M Apr 29 14:25 SRR5345554_2.fastq
==========================================================
Finished on : Mon Apr 29 14:27:30 EDT 2019
0 hours, 2 minutes and 3 seconds elapsed.
==========================================================