-----------------------
Start of variable list:
-----------------------
Sample_ID:
E5-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 19:44:31 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791123
Current job name : Step_02_E5-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/8791123.1.linga

Loading required modules...


List files in scratch directory:

total 118M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:44 SRR6576051_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:44 SRR6576051_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576051_1.fastq <==
@SRR6576051.1 1/1
CGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGG
+
F-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576051.2 2/1
ATGGAAATCCGTGTGTATATTTAAGACCCTGTTGCTCCTCTGGAGCTTGTACGTTCACGAATGATTCATCTGTGTAATAAACTGATTACTACAGTCATTA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576051.3 3/1
ATATAGGAATAGTATGAGCAATAATGTCTATTGGCTTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576051.4 4/1
GCCTGTGAGCCTGGGCTCCCTGCGGGGCAAGGTGCTGCTCATTGAGAATGTCGCGTCTCTCTGAGGCACCACGATCCGGGACTACACCGAGATGAACGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF--FFFF-FFFFFFFFFFF-F--FFFFFFFF-FFFF-FFFFFFF--FFFFFFFFFFFFFFF
@SRR6576051.5 5/1
GTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGAAGGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576051_2.fastq <==
@SRR6576051.1 1/2
NTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-F-FFFFF-FFFFFFFFFFFFFFF-FFF-FFFFFFFFFFF-FFFFF
@SRR6576051.2 2/2
GGTGAGGAAAAATCCACCACTAATCTTAGCTAGACCAAGTTTTTAAATCAAAAAGCCTATTCACACAAAATTATCTGTAATGACTGTAGTAATCAGTTTA
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576051.3 3/2
NTTGAGGGAAGAATGTTATGTTTACTCCTACGAATATGATGGCGAAGTGGGCTTTTGCTCATGTGTCATCTAGGGTGAAGCCTGAAAATAATGGGAATCA
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576051.4 4/2
GCCTTAGGAGTTGCCAGACTGCTGGGACAGCAGGGTTTCTATGTCAGGTTCGATGTCGATGGTACGAAAGCGGCGGCTGTACCTGCGCACGGGAACACCG
+
F8F-FFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFF
@SRR6576051.5 5/2
GTATCAACGCAGAGTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576051_1.fastq

Printing command:
fastqc --outdir SRR6576051_1.fastq

Analysis complete for SRR6576051_1.fastq

Processing SRR6576051_2.fastq

Printing command:
fastqc --outdir SRR6576051_2.fastq

Analysis complete for SRR6576051_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 641M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 321M Oct 12 19:44 SRR6576051_1.fastq
-rw-r--r--   1 kkarri waxmanlab 321M Oct 12 19:44 SRR6576051_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:06 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================