-----------------------
Start of variable list:
-----------------------
Sample_ID:
I7-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 19:41:28 EDT 2018
Running on node : scc-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790817
Current job name : Step_02_I7-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/8790817.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 I7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576437_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576437_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576437_1.fastq <==
@SRR6576437.1 1/1
GNCGTATGATCCAGCAGAAGGAGAGCTTTTACAAGTGGCTATTTTATTTTTCTTTCTGTGGCGAGACTGTCATGGAGCCTGGATATTTCAGGTTCATATG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576437.2 2/1
TAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGCAGGAGCAGGAACAGGATGAACAGTCTACCCACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576437.3 3/1
GTACAGGTGCTCATGTGCAAGAGTAAAGAATATCCAGGAAAACAAAGCGAAATGCACAAAAACGGGTGCCCTGCATACAAGCAAGATGGCGCCACATTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576437.4 4/1
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTTGTTGGGGGGGTGGGGGTTGGG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFF-FFFFFFFFFF-FFFFFFF-FFFF-----FF-F--FF-FFF----FF---FF-
@SRR6576437.5 5/1
GAACGTGCAGTCGCTTCAGAGAAAGCGCTCCGGAGGCCGCAGCATCTACACCATGTTATGGTGATTGTTCCTGTCGATGATGTCCACGGGAGACAGGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-FFFFFFF--F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFF

==> SRR6576437_2.fastq <==
@SRR6576437.1 1/2
NTTTTGTGATGATGGGGATTCTGACCATTTATACCTCATATAAAGAGAAGAGCATCTTCCTTGTGGCCCACAGAAAAGACCCCACAGGAATGGATCCTGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF8F-F
@SRR6576437.2 2/2
NTCCTACTGTGAATATGTGGTGGGCTCATCCAATAAAGCCTAGAAAGCCAATAGACATTATTGCTCATACTATTCCTATATAGCCGAAAGGTTCTTTTTT
+
#-FFF-FFF8FFFF8FF-FFFFFFFFF-F-F--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFF8FFF
@SRR6576437.3 3/2
CCTTGATCCCCAATATCATCACTGGTACCCTGCGAAACATTGCCACTATTTAGGCAACAGGACAGATTTGGCATGGTATGATACTTTATGATGGAGGCAA
+
-FFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFF-FFFF-F-FFFFFFFFF-FFFF-FFFFFF8FFFFFF8FFF8F-FF
@SRR6576437.4 4/2
TAGCAATTCTTCCTTACAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTCTTACAGCCCCTATATTCATAGAACTTATACTAAATAACTC
+
FFFFFFF--FFFFFFFFFFFFF-FFFFFFFFF-FFF-FFF--FFFFFFFFFFFF--FFFFFFFFF--FF--FFFFF-FF-F-FFF-FFF-FFFF8FFFF-
@SRR6576437.5 5/2
GAGGAGAAGACAGCAAAGTACAGGAGGCCAGGAAGTCCTTCTTCTCGGGCCACGCCTCCTTCTCCATGTTCACTATGCTGTATCTGGTGCTCTACCTTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6576437_1.fastq

Printing command:
fastqc --outdir SRR6576437_1.fastq

Analysis complete for SRR6576437_1.fastq

Processing SRR6576437_2.fastq

Printing command:
fastqc --outdir SRR6576437_2.fastq

Analysis complete for SRR6576437_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 151M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 I7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576437_1.fastq
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576437_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:44 EDT 2018
0 hours, 0 minutes and 16 seconds elapsed.
==========================================================