-----------------------
Start of variable list:
-----------------------
Sample_ID:
H9-MAA100138-3_56_F-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 19:46:10 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791257
Current job name : Step_02_H9-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791257.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 92 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:46 SRR6575927_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:46 SRR6575927_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575927_1.fastq <==
@SRR6575927.1 1/1
CNATGTGTCACTCAGTAGGTGCTGGAGATGGATGTCCCAGTGGTGCTTATCCTTGTAGTGGGCATGATATGCTTACGGTGGAAACAGTCTTATTGACCCT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575927.2 2/1
ATTTTCAGGCTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCATCATATTCGTAGGAGTAAACCTAACAATCTTCCCTCAACATTTCCTGGGC
+
FFFFFFFFFFFFF-F-FFF8FFF8FFFFFF8F8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF--FFFF---FF--FFFF-FFFF-FFFFFF--FFFFF
@SRR6575927.3 3/1
TCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTCGTCGACTACGAGTGTGGAGACGAATTGCCA
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFF-FFFFF-F-F----FFFFF-F-FF--F--FF---
@SRR6575927.4 4/1
GCTCTTTCTCGTCATTCGATACTTCTTTGAGCTTTATGTGGCAACACCCCTGGCTGCCCTCCTGAATGTTAAGGAGAAAACCCGACTGCGGGCACCTCAC
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFF-FF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFFF-FFF-FF-FFFF-FFF-FF-F
@SRR6575927.5 5/1
GCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCT
+
FFFFFFFFFF-F-FFFFFF8FFFFFFFFF8FFF8FFFFF8-FFFFFFFFF-FFFFFFFF-FFFFF-FFF--FFFFFFFFF--FFFFFFFFFFFF-FF-F-

==> SRR6575927_2.fastq <==
@SRR6575927.1 1/2
NACTCNAGGTGCTCAATAAATGCTTGTTACATTCTGTTTAGACTCTGTCATTGTGCTCAGCGTGTAGCCTAGCACACAGGGTCAATAAGACTGTTTCCAC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575927.2 2/2
NTATAGAAGAGACAGTGTTTCATGTGGTGTAAGCATCTGGGTAGTCTGAGTAGCGTCGTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAATGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6575927.3 3/2
GGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAAAGTATGCTGCAAACATATGCAGATCCCCTGAGACAGAGTCGCTAACGTTA
+
8F--FFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FF-FF
@SRR6575927.4 4/2
GTGTAGGATCCAGAAAGGCATGATAACCAGCCGAGTTATGATGAAAAATATGGCGAACACAATGAAGAGGTTGTTGCAGGTGTTCTTCCATCCAGCGTAG
+
-FFFFFFFFFFFFFFF8-FFFF-FFFFF-FF--FFF-FFF-F--FFF---F-F--F--FFFFFFF--FF-FFFFF-FFF-F-FFFFF--FFFF---8FF-
@SRR6575927.5 5/2
CTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCA
+
--FFFFFFFF8F88FFFF-FFFFFFFFF-F--FFF---F-FFFFFFF-FFF-FFFFFFFFFF-FF-F-FFFFFFFFFF-FFFFFFFFF-FFF-F-FFFFF

Starting FASTQC command


Processing SRR6575927_1.fastq

Printing command:
fastqc --outdir SRR6575927_1.fastq

Analysis complete for SRR6575927_1.fastq

Processing SRR6575927_2.fastq

Printing command:
fastqc --outdir SRR6575927_2.fastq

Analysis complete for SRR6575927_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 498M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 78 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 249M Oct 12 19:46 SRR6575927_1.fastq
-rw-r--r--   1 kkarri waxmanlab 249M Oct 12 19:46 SRR6575927_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:56 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================