-----------------------
Start of variable list:
-----------------------
Sample_ID:
J5-MAA000907-3_11_M-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 19:49:49 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791340
Current job name : Step_02_J5-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791340.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 102 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:49 J5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  11M Oct 12 19:49 SRR6576470_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  11M Oct 12 19:49 SRR6576470_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576470_1.fastq <==
@SRR6576470.1 1/1
CTATTGTATTGAGCATGGTGACCTGGAGCTGGCAGCAAAGTTTGTCAATCAGCTCAAAGGGGAGTCCAGAAGAGTGGCACAGGACTGGCTGAAGGAGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576470.2 2/1
GTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCAT
+
FFFFF-FFFFFFFFFFFFFFF8FFF8FFFF8FFFFFF88FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF--F-FFFFFF
@SRR6576470.3 3/1
GGCACACCCGTGGGGCTCATTGTCAGCCATCTGCCCTTCGGTCCTACTGCCTATTTCACACTGTGTAACGTGGTCATGCGGCACGACATCCCTGACCTGG
+
8FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFF-FFFF-FFFFFFFFFFFF
@SRR6576470.4 4/1
GTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT
+
FFF-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFF
@SRR6576470.5 5/1
AGGCTTATGAGCAGTCAACCCCACACGCATGACAAACCCTCTCCCACCCCAGCTCATTTGAGTTAATGGAAACACTAACATTCAATACTCTATCTCTGTC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF--FFFFFF-FF-FFFFFFFFFFFFFF-FFFF-FF-

==> SRR6576470_2.fastq <==
@SRR6576470.1 1/2
GTTGCAAACCCTGCAGATACCAATGCTGATTTTCTTTGATATGAAATATGACATTACACAACTCTTCCTAGGCCTTACTCTTGCTGCACTTGAGTGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576470.2 2/2
CTGTGGATGGAAGAATGTTATGTTTACTCCTACGAATATGATGGCGAAGTGGGCTTTTGCTCATGTGTCATCTAGGGTGACGCCTGCAAATAATGGGATT
+
-FFF-F---8FFFFFFFFFFF8-F-FF-FFFF-FF--FFFFFFFFFF-FFFFFF---FFFFFF-F-FF-FFFFFFFFFFFFFFF8--FFFFFFFFF8-FF
@SRR6576470.3 3/2
TTCCAGTGCAGATCTGCAGCCCTACCCCAGCCTGAAGGTGACTATTCAGTCCACTGTCATTAGGTCCTCAACCCATAGATCCTCTGTGGGCTTCAGGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF-F-FFFFFF-FFFFF-FF-F---FFFFF-FFF-FFFFFF-F8--FF-FFFFFF-FF-8F-FF
@SRR6576470.4 4/2
GATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGT
+
FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFF-FFFFF-FFFFF-FFF-FFFFFF-FFF8FFFFFFFF-FFFFF8
@SRR6576470.5 5/2
GTGAAAGCGCGGGGCGGCGGCCGACATGTTCCAGGGCGCGGACAGCCAAGCTGGCAAGTCGGGTTCCAGGTCCATGAAGCCCCCGGGAGGAGAATCGAGC
+
8-FF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-F-FF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576470_1.fastq

Printing command:
fastqc --outdir SRR6576470_1.fastq

Analysis complete for SRR6576470_1.fastq

Processing SRR6576470_2.fastq

Printing command:
fastqc --outdir SRR6576470_2.fastq

Analysis complete for SRR6576470_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 118M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 101 root   root      164K Oct 12 19:49 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:50 J5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  59M Oct 12 19:49 SRR6576470_1.fastq
-rw-r--r--    1 kkarri waxmanlab  59M Oct 12 19:49 SRR6576470_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:09 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================