-----------------------
Start of variable list:
-----------------------
Sample_ID:
J12-MAA000377-3_9_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 19:46:11 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791263
Current job name : Step_02_J12-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791263.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 101 root   root      180K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 J12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  12M Oct 12 19:46 SRR6576369_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  13M Oct 12 19:46 SRR6576369_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576369_1.fastq <==
@SRR6576369.1 1/1
GGCTAGTTTAGGCTATTGTATTGGAGTACATAAGCCATACAAAGAGAGGAAACTGATTTGTTCTCACCCCAGAAGCCCTCATGGCAGGTTTGAATCTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576369.2 2/1
GTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGCAAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576369.3 3/1
GTCTTACGTAATTCAAGTTGGCCTTAAGCTAACCAACCAAGGATGGCCTTGAACTTCTGATCTCCTGCCTCTGCCTGCAGAGCTGGCATTACAGGCAGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576369.4 4/1
ATAGCTGACTTTACACTGCTTTCTTAAAGTGCATAACAACAGATCCTGAAGAAATCCAATAGCTGACTTTACACTGCTTTCTTAAAGTGCATAACAACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576369.5 5/1
ACATGCAACCCTGACTCAAAAGAAAAGGAAAAAGAACTCAACCAAAACCCAGCTCAAGGCTTCCCTGACAATGGGAGAGTCTGACCTCAGGCTTGCATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6576369_2.fastq <==
@SRR6576369.1 1/2
CTTATAAACCTAGTAAACTATACCCCAGTGTCAGACTTTCATGGCATTGCGCTCTGAAGGACTAGAAGTAGAGCCCTGGCAGGCAGGCAGGCAGGAGACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF
@SRR6576369.2 2/2
ATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFF
@SRR6576369.3 3/2
GGTAGAAATGATGCAGCTACCATGCTGTGCATACCTACCATGCACAGTACCCTGCATTTGATTCCCAGCATCATGTGAAACCAAGCACAGCGAAGGCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576369.4 4/2
TCCTGAAGAAATCCAAAACACCATCAGATCCTTCTACAAAAGGCTATACTCAACAAAACTGGAAAACCTGGACGAAATGGACAAATTTCTTCCTGGTTTT
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFF--FFFFFFFFF-FFFFFFFFFFFF-FFFF-FF8FFFFF--FFFFF
@SRR6576369.5 5/2
CTCCAGCTCCCCACCCTTCAGTAGGCGTGGCTTCAGAGGGTGAGTTAGATGAAGACCCTCTTCCCAAGGAGACACTACCCAGACGCAGGTCCACACTCAT
+
FFFFFFFFFFFFFF8FFFFFFF8FFFFFFFF8FFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFF-FFF8FFFFFFF

Starting FASTQC command


Processing SRR6576369_1.fastq

Printing command:
fastqc --outdir SRR6576369_1.fastq

Analysis complete for SRR6576369_1.fastq

Processing SRR6576369_2.fastq

Printing command:
fastqc --outdir SRR6576369_2.fastq

Analysis complete for SRR6576369_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 121M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 90 root   root      180K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 J12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:46 SRR6576369_1.fastq
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:46 SRR6576369_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:33 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================