-----------------------
Start of variable list:
-----------------------
Sample_ID:
G3-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 19:46:08 EDT 2018
Running on node : scc-tl3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791197
Current job name : Step_02_G3-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/8791197.1.linga

Loading required modules...


List files in scratch directory:

total 82M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 37 root   root      132K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:46 SRR6576099_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:46 SRR6576099_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576099_1.fastq <==
@SRR6576099.1 1/1
GCGTAGAATGGCGTATGCAAATAGGAAATATCATTCGGGTTTAATATGGGGTGGGGTGTTTAGTGGATTAGCTGGTATGTAGTTGTCTGGGTCTCCTAGT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFF-F-F-FF-FFFFFFFFFFFFFFFFF
@SRR6576099.2 2/1
CNTCTTTAAAGGCTGCAGCGTCGTCCTCAAATTTCGCACTGACCATAATGTGATCCCTTCCGGCGGTCGGTATAAAATCAGGCAGTTTTTGATCACGTTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576099.3 3/1
AGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGA
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576099.4 4/1
CCTCATTTGAAGAATCAATTAAATGCAGAATTAAATCCGCTTCTTTTACTTCCTCAAGCGTTGAGCGGAATGCAGCAATCAATGTCGTCGGAAGATCCTG
+
F8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF-FFFF
@SRR6576099.5 5/1
CGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGTTTTTTCATGTCCCGCATAATCCTCATTTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF---FFFF

==> SRR6576099_2.fastq <==
@SRR6576099.1 1/2
NCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTCAGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTACCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576099.2 2/2
NAAGACCTCCTGTTTGCCACGCTGGACCCGATGACCAGAAAAATGGTCCTGCCAAGCGGCTACAGTGTTCTTCTTTCAGATACAGTAGGATTTATTCAGG
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576099.3 3/2
TGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576099.4 4/2
CTGTCATTCGCCATAGAAGCCGATACCGTGAAAGAAGAAAGAAAAACGGTGTGCTTCAAATTGCGCTTGTCGGCTATACAAACGCAGGGAAATCAACATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576099.5 5/2
GAATTGGGGCAAGAGGTCCCGGGGAAACGAAACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCAT
+
FFFFF-FFFF8-FFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFF-FFFFFFF8FF-

Starting FASTQC command


Processing SRR6576099_1.fastq

Printing command:
fastqc --outdir SRR6576099_1.fastq

Analysis complete for SRR6576099_1.fastq

Processing SRR6576099_2.fastq

Printing command:
fastqc --outdir SRR6576099_2.fastq

Analysis complete for SRR6576099_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 471M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      132K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 236M Oct 12 19:46 SRR6576099_1.fastq
-rw-r--r--   1 kkarri waxmanlab 236M Oct 12 19:46 SRR6576099_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:36 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================