-----------------------
Start of variable list:
-----------------------
Sample_ID:
D1-MAA100140-3_57_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 19:44:30 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791066
Current job name : Step_02_D1-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791066.1.linga

Loading required modules...


List files in scratch directory:

total 73M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:44 SRR6576015_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:44 SRR6576015_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576015_1.fastq <==
@SRR6576015.1 1/1
TCTGACAGTTGATGAAACATATGTCCCCAAAGAGTTTAAAGCTGAGACCTTCACCTTCCACTCTGATATCTGCACACTTCCAGAGAAGGAGAAGCAGATT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576015.2 2/1
GATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATG
+
FFFFFFFFFFFFF-FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFF-FFFFF-FFFFFFFFFFFFF--FFF
@SRR6576015.3 3/1
AATTTAAACAGGTCACCAAAGAGACCAGAAGTAATTAAAGAGGTATATTTACAGTAGCACATCACAGTAAACGGAAAGCATTCACAGTTTCAACATCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576015.4 4/1
TTCTCAAAGTATGCCTTGGCCTGGCTCTGAATCTCTGAGGTCTTGGCCTTCTCCATCAAATCTTTGCCATAATCAGTCATGCTCTGAAAGTATTGAGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576015.5 5/1
TCTCACAGGAATGTGGCCCATCAACACCCTGAGATGTGTCCCCAGAGTATGTCCTTTCGCTGGAATCTTAGAAAATGGAATTGTACGCTACACGAGTTTT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFF--F-FFFFFFFFFFFFFFFF-FFF

==> SRR6576015_2.fastq <==
@SRR6576015.1 1/2
NCTAGTGACAAGGTTTGGACCCTCAGTCGAGAAGCAGGTGTCCTTGTCAGCAGCCTTGCAACATGTATCCAGGAACTGTGCAAAGTCATCCATGACAGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6576015.2 2/2
CAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCATCTAAGAAGTTGGGGGACGCCGACCGCTCGTGGGTCGCGTAACTAGTTATCAT
+
FFF---FFFFFFFFFF8FFFFFFFFFF-FFFFFF--F-FFFFFFFF-FFF-F-FFF-F-FFFFFF-FFFFFFFFFF--F-FFFFF-FFFFF-FFFF-F-F
@SRR6576015.3 3/2
GATGAGATCAAGGATAACTCAAATGCATCTAACAACAACGGATTTATTGCACCCAATGAAAATCCAAACCCAGAGGAGGCTTTAAGAGAGGATGCTGCTG
+
FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFF8FFFFFFFFFFFFFFF
@SRR6576015.4 4/2
TCCTAGGCCATAGTCTGCCATCATGAAGCTGCTCGCACTGGTCGCACTGCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAGAGACAGGCAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFF8F
@SRR6576015.5 5/2
CCCATTTTCTGGCCTCGGAGGGAAGGGACATTTTACTTCCAGGCATTCTGGCAATCGGGTCCAGTTTCCTTGTTCTGTGCACATGACTGTGTCATTTCCG
+
F-FFFF-FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFF8FFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576015_1.fastq

Printing command:
fastqc --outdir SRR6576015_1.fastq

Analysis complete for SRR6576015_1.fastq

Processing SRR6576015_2.fastq

Printing command:
fastqc --outdir SRR6576015_2.fastq

Analysis complete for SRR6576015_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 392M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 196M Oct 12 19:44 SRR6576015_1.fastq
-rw-r--r--   1 kkarri waxmanlab 196M Oct 12 19:44 SRR6576015_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:11 EDT 2018
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================