-----------------------
Start of variable list:
-----------------------
Sample_ID:
B5-MAA000907-3_11_M-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 19:41:27 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790730
Current job name : Step_02_B5-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790730.1.linga

Loading required modules...


List files in scratch directory:

total 35M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 81 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576014_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576014_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576014_1.fastq <==
@SRR6576014.1 1/1
ATAATAGACTTCAGCATGCTGCATTGCTCGAATGGCCCAAGCCATTTCAATATCAGGGTCGTTGCCATATGACTCCGGAGGGTGAGAGAGCGCATGGGCG
+
F-FFFFFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF-FFFFF-FFF-FFFF
@SRR6576014.2 2/1
GTACATGGGGAACTCACATTCAAGCTGGGTGGTGGTGGCGCACGCCTTTAATCCCAGCGCTTGGGAGGCAGAGGCAGGCAGATCTCTGAGGCCAGCCTGG
+
FF8FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6576014.3 3/1
GGCCACTTAGCCTTTAGTGCAAGAAGATAAGTGAAGGTCTCCAAACTATAGTAACCTCTGTCTACAAAATCACCCATAAATATGTAGTTTGTGTCAGGAA
+
FF-FFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576014.4 4/1
TTGTAGCTCAGGATATGGTCTAGCCTGGTAAATGGCCATGGCCACTTAAGAGCGCATCCTGATGCCACGTAGTGTTGAGTTTCAGTTCTTCATTCCTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576014.5 5/1
GTGTGTGTGGTGTGGTGTGTGTGTGTGTGTGTGTATGGGTGTGGTGTGTGTGGGTGTGGTGTGTGTGGTGGTATTTGTATGTTTTTTAGGTTATGTGGCT
+
FF--FFF-FFFFFFFFFFFFFFFF888F8FFFFF8F88FF--8FFFFFFFFF--FF--F-FFFF------F----FFF--F------------FF-F-FF

==> SRR6576014_2.fastq <==
@SRR6576014.1 1/2
NTACATGGGAGGTCACTTCCGGGACGAGAAAGCCGCACTTACCTAGCGGCGACATGGATGCTGCCGGCGAAAGCGAAGAGCCGGTCTCTGGGGAAGCGTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576014.2 2/2
GTATAGCCCTGGCTGTCCTGGAACTCTCTCTGTAGACCAGGCTGGCCTCAGAGATCTGCCTGCCTCTGCCTCCCAAGCGCTGGGATTAAAGGCGTGCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576014.3 3/2
GATTCGGCCTCCGCCGCTGCCTCCGCTACTACAGCCGCTGCCGCTGCTGTCGCCGCGGCTTGTTCTTCCTAAAATGGCGCCGCTGGATCGGGCCAAGTAT
+
8FFFFFFFF8FFFFFFFF-FFFFFFF-FFFFFFFFFF-FFFFF--FFFFFFFFFFF-FF-F-FFF----FFFFF-F-FFFFF--FF--F-FF-F----8-
@SRR6576014.4 4/2
GGCTATAGTACTACAAGATAAACTAGACTTCAGAGCAAAGGACCTTACTAGGAAAATACTTGGGATATGCCAATTCAGCATGTTTATTTGCCAATGAGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576014.5 5/2
CCACATACACACACACACATACACACACACACACACACACCACACACACACACACCACACACAAACACACACACACACACACACCACACCACACACACCA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFF-FFFFFFF--F--F-FFFFFFFFFFFFF-F--FF-FF--F-FFF--

Starting FASTQC command


Processing SRR6576014_1.fastq

Printing command:
fastqc --outdir SRR6576014_1.fastq

Analysis complete for SRR6576014_1.fastq

Processing SRR6576014_2.fastq

Printing command:
fastqc --outdir SRR6576014_2.fastq

Analysis complete for SRR6576014_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 170M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 B5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  85M Oct 12 19:41 SRR6576014_1.fastq
-rw-r--r--   1 kkarri waxmanlab  85M Oct 12 19:41 SRR6576014_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================