-----------------------
Start of variable list:
-----------------------
Sample_ID:
A2-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 19:42:18 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790924
Current job name : Step_02_A2-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/8790924.1.linga

Loading required modules...


List files in scratch directory:

total 86M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  43M Oct 12 19:42 SRR6575724_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  44M Oct 12 19:42 SRR6575724_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575724_1.fastq <==
@SRR6575724.1 1/1
TACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575724.2 2/1
TGCCTGTGACGGCCCGTGTGGTGTTCATTTTTGGCCCTGACAAGAAACTGAAGCTGTCTATCCTCTACCCTGCCACCACGGGCAGGAACTTTGATGAGAT
+
-F-8FF-FFFFFFF8FFFF88FFFFFFFFFFF888FF8FFFFF-F-FFFFFFFFF-FFFFFF-FF-FFF-FFFF--FFF-F-FFFFFFFFFFFFFFFFF-
@SRR6575724.3 3/1
GAGTTGTTCCTGGATACCGTGTATGGAAACTGCTCAACTCAGGTTACCGTGAATTCAAGAAAGGGAACCGTACCAACAGAAATGTCCACAGAGAGAAACC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6575724.4 4/1
CTCCCCATGAATATAATAGTGTTCAGTGCAACTTCCCTTATAAGAACCAGGAAGGGCCTGTTGGCCTTGAAGGTCACCCTATTGGGGTTCAGTGACCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575724.5 5/1
TGTCTGTCCTGACGCCACTGCTGCTGAGGAGCCTGACCGGCTCGGCCCGGCGGCTCATGGTGCCGCGGGCTCAGGTCCACTCGAAGCCGGCGCGGGAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575724_2.fastq <==
@SRR6575724.1 1/2
NATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGC
+
#FFFFF-FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575724.2 2/2
NGCCACGAACTTTCTACGGACCTGCTGCAAGGACCCACGGCTGCCAGCTGACATCCTCAGGCCCCAGTACTGGATGTGCAGATGCAGCCCCAATTTCCGC
+
#--FFFFF-F8FFF8FFFFFFF-FFFFFFFF-F-FF-FFFFFFFFFFFFFFF--FFFF-F-FFFFF-FFFFF-F-FFFF-FFFFFFFFFFFF--88FFF8
@SRR6575724.3 3/2
NTTCAATCAGCTGTGGCAAGAGGGATGTGATTGCTTCACCAGTGAGACCTCTCAGCTCAGTAACCAGTTTATTGAAGAGATTTGCTCTCTGAGCATTCTG
+
#FF-F-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFF-FFFFF-FFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-8--FFFFFF
@SRR6575724.4 4/2
NGGGGATGACATCACCATGGTGCTCATCCTGCCCAAGCCTGAGAAGAGCCTGGCCAAGGTGGAGCAGGAGCTCACCCCAGAGCTGCTGCAGGAGTGGCTG
+
#FFFFFFFFFFFF8FF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575724.5 5/2
GAATTGAATAACATGATCCCGGGGAAGGCCAGCCAGGAATGCAGGCAACATGATCAAGGTGGGCTGGCAAAAGTGGTCTAGTCAAAGGATGAGGGAAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575724_1.fastq

Printing command:
fastqc --outdir SRR6575724_1.fastq

Analysis complete for SRR6575724_1.fastq

Processing SRR6575724_2.fastq

Printing command:
fastqc --outdir SRR6575724_2.fastq

Analysis complete for SRR6575724_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 458M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 229M Oct 12 19:42 SRR6575724_1.fastq
-rw-r--r--    1 kkarri waxmanlab 229M Oct 12 19:42 SRR6575724_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:59 EDT 2018
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================