-----------------------
Start of variable list:
-----------------------
Sample_ID:
O11-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 19:42:17 EDT 2018
Running on node : scc-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790880
Current job name : Step_02_O11-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/8790880.1.linga

Loading required modules...


List files in scratch directory:

total 4.4M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 97 root   root      128K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 O11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.1M Oct 12 19:42 SRR6576958_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.2M Oct 12 19:42 SRR6576958_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576958_1.fastq <==
@SRR6576958.1 1/1
GAAGAGAACAAGATGCACAGATACATGCAGTGCAACTCAAGCTAGGACTCTGAGAGAGAAAATGATGAGTAGATATTTAAAGTGTAATCTGTTAAAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576958.2 2/1
ATGTAGACCAAGAGGGACTCGAACTTATAGATCCACCTGTCTCCGCCTCCCAAGCGCTGGGATTAAAGATGTGCACTACTATGCCCATCTTACTTAAATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576958.3 3/1
CCAGAGCACTGTCTTATCTTGGTGCTCCGGACCCTCCACTGCTGTCGGCCCCGAACGCCCTTGGTTCCTATATTCTCCTGCTTAGAAGCTGGTCTGCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576958.4 4/1
AGACAGAGGAAGCCATTGACAGAATTTTTGCTATATCCCAGCAACAGCGGCAGCAGCGAGGCAAGTCGAAGAAAAGCCGAAAGGCGGGTAAGCATTACAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576958.5 5/1
GTACATGGGAGGGAAAGCACAGCAGCAAGGACAGTTGTGGCAGCAGGAGGTTGAGCCACTTCCTTGCATTTTCAAATCAGAAAGCAGAGATAGGACAGGA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF

==> SRR6576958_2.fastq <==
@SRR6576958.1 1/2
GTCAGGGTCTGCAATTGCTTGACAGTGTGCGGAAAACCTCCCATCCTTATGTAGCTGACAGGGGCTTTTCGCGGAGGAGAAAGACACTGAATCCTGTCAG
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFF-FFF
@SRR6576958.2 2/2
GCGTTGGGATATTTAACAACCAAGATTTCTTCCCAGGTTTGAGATTTGGGTTATTATTCTGATGTGTCTGATTTCTCGATTATATATCTCTGTGTTGGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576958.3 3/2
GTGTAGACCAGGCTGTCCTCGAGCTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACCGCCCGGCTCTGACCAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F8
@SRR6576958.4 4/2
GAGTCCTCTGGAAATAAGTCAGTTGCATTGCCAGCATGACAAAGAAGATGGCAATGTTGAGGATCAAGAAGAGTCTGGTGTAGGAGGCTGACAGTGAAGG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF
@SRR6576958.5 5/2
AGCAATAGCTGCCTGGGGGTTCAGCCGATGAAGAATTTGTAGGCTTAGTTTTAATTCCCTCTTACTAGTGTTCAACATGGTGGTCATGGCCAAGGCCAAT
+
FFFFFFFFFFFFF88FFF888FFFFFFFF8FFFFFF-FF--FFFFFF--F-FFFF-FFFFFFFFFF-FF-F-FFFFF-FFFF--FFFFFF-FFFF-F8F8

Starting FASTQC command


Processing SRR6576958_1.fastq

Printing command:
fastqc --outdir SRR6576958_1.fastq

Analysis complete for SRR6576958_1.fastq

Processing SRR6576958_2.fastq

Printing command:
fastqc --outdir SRR6576958_2.fastq

Analysis complete for SRR6576958_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 22M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 101 root   root      128K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 O11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  11M Oct 12 19:42 SRR6576958_1.fastq
-rw-r--r--    1 kkarri waxmanlab  11M Oct 12 19:42 SRR6576958_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:32 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================