-----------------------
Start of variable list:
-----------------------
Sample_ID:
J18-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 19:41:28 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790824
Current job name : Step_02_J18-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/8790824.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 J18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576414_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576414_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576414_1.fastq <==
@SRR6576414.1 1/1
CNACTGGACTCAACCCCTAGCCTCTGTTTTTGTCCTTTTAACAAAAAGTCATTTTCACAAGTTTAAATAGCAGAAGGCAGACTTTAAAACTCAGCTAACA
+
F#FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576414.2 2/1
ACCTAAATTATCCAGGCTGGCCTTGAACTTTTGATCCTCCTGCCATGGCTCCCAATTATCCTGGATGACAGGATTGCACCTGAGATACTCTCCCTGCTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576414.3 3/1
ACCCAACAGGACTGGTTCTTCAGATCCCTGGGATGTGCCCAGACAGATGGGCAAGGACACGGGGAGACTCTGTGAGGCCAGGGTACCTGAGCACTCTCTG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFF-FFF
@SRR6576414.4 4/1
GTTAGCACACCCCAGGGACCTATTAAAAATGCAGTTTCTCAGACTCATCACAGAGAGACTCAGAAACTCAGCAGCTTGTGCCCAGCTGACTGACACATGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576414.5 5/1
CCTTGGTTTTATGCAAGCGTAAAGGAATCACAGACGTCCAGGCCCAGCTCCTCTGGTTCCTACAGACTTTTCTGTTTGGTGTAGCCTCTCTCTCCATCCT
+
F-FFFFFFFFFFFFFFFFF8F8FFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFF--FFFF-FF-FFFFFF-F-FFFFFFF-FFFFFFFF

==> SRR6576414_2.fastq <==
@SRR6576414.1 1/2
NTATCAACGCAGAGTACATGGGATTTGTTTGTTTGTTTTTTAACTTCCTCCTTGGGTTGTAACAGGATTTGTTGTCTAGCTCCCACAGCCTGCTGAGCTC
+
#FFFFFFFFFFF8FFFFFFFFFFFFFF88FFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576414.2 2/2
GTGGTGTGCGGTTCCTGCCAAACCCTGTCTACGTGCTGGCAAGTTTCCAAGGACATTCCCAGCCTGGGACCAGCAGCGGAAGAGATCGACACAAAGACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF
@SRR6576414.3 3/2
CCAGAGTACAGCCCGCATCTCCTCATTAGAGCAATCTGGGAGGTGGTCACTCCACCTACACTCACTTTAGTCATGATAAAACCAAGACATAGAGGACACT
+
FFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FF8F-FFFFFFFFF
@SRR6576414.4 4/2
ATGGAGTTCAAGTTGAAGCCATAAACCAAAAGCCAAAAACTTGGCTGCCACATGTGTCCTAATTGCCCATGGGGCTGCCTTTGCTCTCAGTGCATAGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FFF
@SRR6576414.5 5/2
CCTCTAACAAGGCCACATACCTCCTAGTAGTGCCACTTCCCAGGGGCCAAGCATATTCAAACCACCACACAGAGCATAGGTGCACCCACAAATAAATCTA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FF8F8FFFFF--FF-FFFF-FFFFFFFF-FFF-FFFFFFF-FFFFF-FFFFFFFFFFFF--FF-----8

Starting FASTQC command


Processing SRR6576414_1.fastq

Printing command:
fastqc --outdir SRR6576414_1.fastq

Analysis complete for SRR6576414_1.fastq

Processing SRR6576414_2.fastq

Printing command:
fastqc --outdir SRR6576414_2.fastq

Analysis complete for SRR6576414_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 184M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 J18-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:41 SRR6576414_1.fastq
-rw-r--r--   1 kkarri waxmanlab  92M Oct 12 19:41 SRR6576414_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:55 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================