-----------------------
Start of variable list:
-----------------------
Sample_ID:
N6-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 19:49:50 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791391
Current job name : Step_02_N6-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/8791391.1.linga

Loading required modules...


List files in scratch directory:

total 32M
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 N6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  16M Oct 12 19:49 SRR6576650_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  16M Oct 12 19:49 SRR6576650_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576650_1.fastq <==
@SRR6576650.1 1/1
CCTTATGGGTTGGCCTGTAAACTTGTATAGTCCCATCATTACTGAAAAGCTGAAGGCAGACATAAGCAGAGCCTAAGTTAGGAGAGAGCCTCACTGACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576650.2 2/1
GCAGTGGGCAGGCAGACATGGTGCTGGAGGAGCTGAGAGCTCTACATCTTGAACCAAAGGCCACCAGAAGACTGTCTTCTCCAGGCAGCCTGGAGCCTAA
+
F-8FFFFFFFFFFFFFF8FFFFFFFFFFFFF8F8FFFFFFFFFF-FFFF--FFFFF-F-FFF-FFFFFF-FF-F-F--FFFFFFFFF-FFFFFF-FFFFF
@SRR6576650.3 3/1
AGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCAGTAAATCAGTTATGGTTCCTTT
+
FFFFF-FFFF-FFF8-F8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF--FFFF-FFFFFFFFFFF--FFF-FFFF-F-FFFF-FF-F-
@SRR6576650.4 4/1
GATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFF-FF
@SRR6576650.5 5/1
GTTCTAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCTGGGGCTACACAGAGAAACCCTTTCTCGAAAAAAATAATAAAGTTGTATGTGAAATTA
+
F8---FFF-FFFFFFFFF8FFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFFF-FFFFFF-FF--FFF--FFF-FFFF-FF-F-FFF--FF-F-FFF----

==> SRR6576650_2.fastq <==
@SRR6576650.1 1/2
GAATATAGGTCTGTCTGCACATGTTGCCTTCCATGTCTGACTAGACAGTGACACTGACCAATTCTGTCACGTCCTCATGCAGAGAAACAAGCCTATGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576650.2 2/2
AGTACACTGTAGCTGCACAGATAGTTGGTGGGAATTGAACAAGGGCTCACTCTGGTCAGCCCTGCTCCCTCTGGTCAACACTGCTCGCTTGCTCAGACCC
+
FFFFFFF-FFFFF8FF8FF8FF-F-FFFFF-FF-FFF-FFFF--FFF-FFFFFFF-FFFF-FFFF-FFF-FF-FF-FFF-F--F-FFF-FFF-F-F--FF
@SRR6576650.3 3/2
CCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576650.4 4/2
TGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576650.5 5/2
GCCTAATTACCAAACATACAAAGGAAGAGATTAAAACACTCACTTCAAATCAAACAGGGCTTCTTACCTACTGTTTTCCACAGCCTTCATGGCATATTCA
+
F-FFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFF-F-FFFF-FFFFFFFFFFFF----FFF-FFFFFFFFFF-FFFF-F-FFF-FFFFFF--FF-FFFF

Starting FASTQC command


Processing SRR6576650_1.fastq

Printing command:
fastqc --outdir SRR6576650_1.fastq

Analysis complete for SRR6576650_1.fastq

Processing SRR6576650_2.fastq

Printing command:
fastqc --outdir SRR6576650_2.fastq

Analysis complete for SRR6576650_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 162M
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 N6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  81M Oct 12 19:49 SRR6576650_1.fastq
-rw-r--r--    1 kkarri waxmanlab  81M Oct 12 19:49 SRR6576650_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:13 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================