-----------------------
Start of variable list:
-----------------------
Sample_ID:
H12-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 19:49:49 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791381
Current job name : Step_02_H12-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/8791381.1.linga

Loading required modules...


List files in scratch directory:

total 47M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 33 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 H12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:49 SRR6576258_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:49 SRR6576258_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576258_1.fastq <==
@SRR6576258.1 1/1
CTACTCACTTAATGTACCTGTGTACAGGGACACGTCATTTTACATACTTACGAGGTGCAGGCTGATTACTTGAGATGGGTTATGATCAAGTCTGGGTAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576258.2 2/1
GAACTATTGATTCAATGTTGGGTAGTGAATCAGGAAGTCAGCAACCTAGGAGAGGCTCTGTGTGAGAACGGCTTCCCTCACTGTGTGAAGAACAGAGGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576258.3 3/1
CCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCCATAGAAGCCGATACCGTGAAAGAAGAAAGAAAAACGGTGTGCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576258.4 4/1
GTAGGCAGCAATATCCTTCTCATACTTCTCCTTCAGCTTGGCAGCTTTCTTCTCATAGGGCTGCTTGTCATCTGCTGCAGTGTTGTTCCACATCTCTCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-
@SRR6576258.5 5/1
GGGTGTAGGCGCCAATATCACAAAGCTACATAAATAGAAGTGAGCCTTAGCAAGGTCACTTCCTGTTTTCCGATGACGACGTTAGCATAGCCCCATGAAA
+
FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF

==> SRR6576258_2.fastq <==
@SRR6576258.1 1/2
NGCAGAGTACATGGGAAACAACTCCTCAGCCAATAGATTCACAGAACCATGTGGCAAGAAACAGAAACATAAGCACGCCTTGGTCTGCAGGAGCTCCAAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576258.2 2/2
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTTTTTAAATAAAAAATTTTTAATTAAAAAAAATTGTTTAAAATAATTTGGTGTGTTGTTTTTTA
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8-FFFF-F--FF-F-F-F-------FF-F-FF-------FF--F----F-----------8FF---8
@SRR6576258.3 3/2
GTATCAACGCAGAGTACTTTTTTTTTTGATCACGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF8FFFFF
@SRR6576258.4 4/2
GCGCCGGGGCAAGCGCGAGCCGGACGGGCACTGGGCGACTCTGTGCCTCGCGGAGGAAATTCAACTAAACATGGGCAAAGGAGATCCTAAAAAGCCGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF-FFFFFF-FFFF-F8FFFFFFFF-
@SRR6576258.5 5/2
TGCTAACTCTAAAACAATATTTTAGAAACAGCCTGAGGAGTGTTAGCATTTGTGCTCTCGTCCAGAAAACAGGTTTTCGTTTGAAAACCTGTCTGTAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576258_1.fastq

Printing command:
fastqc --outdir SRR6576258_1.fastq

Analysis complete for SRR6576258_1.fastq

Processing SRR6576258_2.fastq

Printing command:
fastqc --outdir SRR6576258_2.fastq

Analysis complete for SRR6576258_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 242M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 33 root   root       20K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 H12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 121M Oct 12 19:49 SRR6576258_1.fastq
-rw-r--r--   1 kkarri waxmanlab 121M Oct 12 19:49 SRR6576258_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:08 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================