-----------------------
Start of variable list:
-----------------------
Sample_ID:
I9-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 19:47:49 EDT 2018
Running on node : scc-wm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791333
Current job name : Step_02_I9-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/8791333.1.w

Loading required modules...


List files in scratch directory:

total 32M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 28 root   root       12K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 I9-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:47 SRR6576325_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:47 SRR6576325_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576325_1.fastq <==
@SRR6576325.1 1/1
ATCCAAGTCCATGACCATTAACTGGAGCCTTTTCAGCCCTCCTTCTAACATCAGGTCTAGTAATATGATTTCACTATAATTCAATTACACTATTAACCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.2 2/1
AATTATCTTCGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTCGTCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.3 3/1
GTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.4 4/1
CATTTATAGAAACCTGAAACATTGGAGTACTTCTACTGTTCGCAGTCATAGCCACAGCATTTATAGGCTACGTCCTTCCATGAGGACAAATATCATTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.5 5/1
CATCTAATCCTACTGTGAATATGTGGTGGGCTCATACAATAAAGCCTAGAAAGCCAATAGACATTATTGCTCATACTATTCCTATATAGCCGAAAGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFF-

==> SRR6576325_2.fastq <==
@SRR6576325.1 1/2
GATTTATGTGGTTTCGTTTACCTTCTATAAGGCTATGATGAGCTCATGTAATTGAAACACCTGATGCTAGAAGTACTGAAGTATTAAGTAGTGGGACTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFF
@SRR6576325.2 2/2
GTTGGATTTTAATTCTATTTATTTATTTATAGTTGACACGTTTTACGCCGAAGATAATTCTGTCTCTTATACACATCTGACGCTGCCGACGAAGCAAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.3 3/2
TTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGC
+
FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.4 4/2
GAACGATTGCTAGGGCCGCGATAATAAATGGTAAGATGAAGTGGAAAGCGAAGAATCGGGTCAAGGTGGCTTTGTCTACTGAGAAGCCCCCTCAAATTCA
+
FFFFFFFFFFF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576325.5 5/2
AGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACCTTTCGGCTATATAGGAATAGTATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576325_1.fastq

Printing command:
fastqc --outdir SRR6576325_1.fastq

Analysis complete for SRR6576325_1.fastq

Processing SRR6576325_2.fastq

Printing command:
fastqc --outdir SRR6576325_2.fastq

Analysis complete for SRR6576325_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 183M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 28 root   root       12K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:48 I9-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:47 SRR6576325_1.fastq
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:47 SRR6576325_2.fastq
==========================================================
Finished on : Fri Oct 12 19:48:02 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================