-----------------------
Start of variable list:
-----------------------
Sample_ID:
D5-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 : 8790754
Current job name : Step_02_D5-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/8790754.1.linga

Loading required modules...


List files in scratch directory:

total 37M
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 D5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576230_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576230_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576230_1.fastq <==
@SRR6576230.1 1/1
GGGCACCCCCACGGAGCCCAGAGGCCTGGCCAGAGGGGGAAGGCACAAGAGCATGGGGATTGGGGGCACAAGCACCCCCCTCCGAAGCCCAGGGGGCAAG
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576230.2 2/1
GGATTTAAAGTGGACTCATTCCAATTACAGGGCCTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F---FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576230.3 3/1
ACTCTTAGCTAAGGAACTTCTGATGACACTCTGTTTGAGAGCAGGGACCTAGAAATCACTGTCTCCACAGACGTTATGTATAAATTTTAATCACCACATC
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576230.4 4/1
GGGCTATAACGTCTGCATACTATCGTGGAGCAGTAGGTGCCTTATTGGTTTATGACATTGCTAAGCATCTCACATATGAAAATGTAGAGCGATGGCTGAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576230.5 5/1
CCTAGCATAAACCACGGACTCAATTTGCTTCTGTTGGAGTGGGGCCTGCAGCAAGCTCAGCCTCAGCTCTGGGATTCGAGTGCCTAATGGCCACCGAGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576230_2.fastq <==
@SRR6576230.1 1/2
NCCCTGCCCTTGCCAGCTGTGCCCACCTTTGTATTTAGTTTTGTAGTTTCTTGGCTTTTATAATCCCCTTTTTCTTGCCCCCTGGGCTTCGGAGGGGGGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576230.2 2/2
GATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFFFFFFFFFFFF-FFFFFF
@SRR6576230.3 3/2
CAGAAGAGCAGATGGTGCTCTTAACTGTTGAGCCATCTCTCCAGCCCCAAACATAAAGTTTTTAATTAACAAAAGATTGTCTTAAAATATTGTATAACAA
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-FFFFFFFFFFFF
@SRR6576230.4 4/2
ATGAATGACAAACCATTCTTCTCTGCAAAAGCTCTTGCTTCATCTGTAGGAACTGCCCTGAGATGACGTAAATCACTCTTATTGCCCACAAGCATGATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576230.5 5/2
GTTCCAGTGGCGATTCTCCCGGAACGAGATCCACGGCAGGCAGACAAGGAAATCCAAAGGGAAACTCAGTGCCAGCAACAAGCAGCAAGCAGAAGAGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFF

Starting FASTQC command


Processing SRR6576230_1.fastq

Printing command:
fastqc --outdir SRR6576230_1.fastq

Analysis complete for SRR6576230_1.fastq

Processing SRR6576230_2.fastq

Printing command:
fastqc --outdir SRR6576230_2.fastq

Analysis complete for SRR6576230_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 197M
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 D5-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:41 SRR6576230_1.fastq
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:41 SRR6576230_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:54 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================