-----------------------
Start of variable list:
-----------------------
Sample_ID:
H5-MAA100140-3_57_F-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:46:10 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791247
Current job name : Step_02_H5-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791247.1.linga

Loading required modules...


List files in scratch directory:

total 50M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 92 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:46 SRR6576130_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:46 SRR6576130_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576130_1.fastq <==
@SRR6576130.1 1/1
GATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576130.2 2/1
GACTGGGCGTGTGTTAAGCATTTGTGATGGTATTGCGCGAGTGCACGGGCTGAGGAATGATCAAGCAGAGGAGATGGTGGAATTCTCTTCAGGCTTAAAT
+
FFF8F--F-----F8FF8FF8F8FFFF88888FFFF8FF8-F8-F-F--FF-FFFF--F-FFFFF-FFF--F-FF--F-FF-F-FFFFFF-F--FFFFF-
@SRR6576130.3 3/1
ACTATGCGCAGACGCTTGAAACGATGTGACATCGCTTCTAGAGTATGAGCCGCAATGCACGACTGATACTCGATATGAGCAGCAGTCGGCTATGATTTGC
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576130.4 4/1
AGATTGGCGCTAGTAGATCACAGAACAACCGCCGCATACGGCCGATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCTAAACCGACGCA
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFF
@SRR6576130.5 5/1
GAGATCAGCTTCAAGCTCTTCCACGAGTGCCTTCAGCTCTTCTACCTTCCCTTTTCCTATATATGTAGCGGCGTCAGCCCTGTTCCGTTTTTGTGTGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8FFFFFF--FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFF--FFFFFFFFFF

==> SRR6576130_2.fastq <==
@SRR6576130.1 1/2
ACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGG
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF
@SRR6576130.2 2/2
TATATGATCAAAGCGTGCTTGCCGTTTTCTCTAAAGAACTCTCCCAGGGAGAAGCCGGAGTAGGGAGCCCAATACTGAAGCGGGGAAACGTCAGATGCAT
+
8F-FF-F-FFFFFFF-8-FFF8FF-F-F--FF-F---F-FFF-FFF--FFF-FF--FF--FF-FFF-F--F-F-FFFF-FF-F-----FFFFF-FF-8F-
@SRR6576130.3 3/2
ACCGAGTCGTTCTGATAGATCCCGCGTCAGGCAAATAATAAGCGCAAGCAGATAGCATCCGAGCTAATGTATCAGCCTATACGCTAATTTCAGAGTCTTA
+
FFFFFFFFFF8-88FFF--F8FFFFFFFFFFF--F-FF-F-F-FFFF-F--FFF-FFF-FFFFF-FFFFFF-FFFFF-F-F-FFFFFF----F-FFF-F8
@SRR6576130.4 4/2
GTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTACCAGCTCGATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576130.5 5/2
TATCAACGCAGAGTACATGGGGGGAATTCGAGCTCGCATTTTGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAAAGTACTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6576130_1.fastq

Printing command:
fastqc --outdir SRR6576130_1.fastq

Analysis complete for SRR6576130_1.fastq

Processing SRR6576130_2.fastq

Printing command:
fastqc --outdir SRR6576130_2.fastq

Analysis complete for SRR6576130_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 293M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 78 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 147M Oct 12 19:46 SRR6576130_1.fastq
-rw-r--r--   1 kkarri waxmanlab 147M Oct 12 19:46 SRR6576130_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:43 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================