-----------------------
Start of variable list:
-----------------------
Sample_ID:
D9-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 19:44:30 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791093
Current job name : Step_02_D9-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/8791093.1.linga

Loading required modules...


List files in scratch directory:

total 8.6M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 4.4M Oct 12 19:44 SRR6576237_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab 4.1M Oct 12 19:44 SRR6576237_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576237_1.fastq <==
@SRR6576237.1 1/1
GGGCTGCACGCGCGCTACACTGACTGGCTCAGCGTGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576237.2 2/1
TATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGAAAAATGCCTCTCTCTTATAC
+
F--FFFFF-FF-FFFFFF888FFFF8FFF8FF8FFFFFFFF-FF-F-F-FF-FFFFF-FF-FFF-F-FFF--FFFF---F-FFFFFFFF---FFF-FFFF
@SRR6576237.3 3/1
AAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFF-FFFFF
@SRR6576237.4 4/1
TACCAGTACTGATTGCCGAGCAAATCTGTGAATGGCGACTATGCGCCTAGTCAACCAGATGTGTGCTAGCCCGTCGAGACTGAAAAGCTATAACCCGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576237.5 5/1
TATCAACGCAGAGTACATGGGCAGTGGTATCAACGCAAAAAAAAAAAAAAAAAAAAAAGAAATACAGTATCTTTAAAAACAAACCGAGCCCAACTAAAAA
+
FFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF--------------F--FFF--FFF-F---F-----------

==> SRR6576237_2.fastq <==
@SRR6576237.1 1/2
AATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFF8F
@SRR6576237.2 2/2
GCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATACTGTCTCTTATAC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF8FFF
@SRR6576237.3 3/2
GTCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576237.4 4/2
GCCGTACGCTGAGGACCACCTGAAACGGGCATCTTCGCTCTTCGTTGTTCGTCTACTTCTAGTGTGGAGACGAATTGCCAGAATTATTAACTGCGCAGTT
+
FFFFFFFFFFFFFFFFFF-8FFFFF-F-F-FF--F-FFFFFF-FFFFFFFFF--FFFFFFFFF-F-FF-FF-FFFF--F--FFFFFFFFF-FF-F-FFFF
@SRR6576237.5 5/2
GAGTACTTTTTTTTTTTTTTTTTTTTTTTCGTTTATAACACAGCCCAATTTATAAGCGTTTTAAAATTGAAATATAAACAAAATAACCAGCCCACCCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF----F---FF-----FFF---F----------F--FF----------FFF--F--F-------F--------

Starting FASTQC command


Processing SRR6576237_1.fastq

Printing command:
fastqc --outdir SRR6576237_1.fastq

Analysis complete for SRR6576237_1.fastq

Processing SRR6576237_2.fastq

Printing command:
fastqc --outdir SRR6576237_2.fastq

Analysis complete for SRR6576237_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 53M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 112 root   root      116K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  27M Oct 12 19:44 SRR6576237_1.fastq
-rw-r--r--    1 kkarri waxmanlab  27M Oct 12 19:44 SRR6576237_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:50 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================