-----------------------
Start of variable list:
-----------------------
Sample_ID:
G11-MAA000377-3_9_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-tk4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790785
Current job name : Step_02_G11-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790785.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 39 root   root       52K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576192_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576192_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576192_1.fastq <==
@SRR6576192.1 1/1
GTAATAGTGAGAATGTGCCAAGCAGGCAAACAGCTGGGGAGGGCACAGGAAGCAGGACACACACACACAGCAAGACAGAGGGACAGAGGCACAGGCAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576192.2 2/1
GCGGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576192.3 3/1
TCACAGGTATGTGCCCACCATGTCCAGCATTGTACATAAATGCCAGGCATCTAACCTCAGGTCCTTAAACTGTGTGGCAAACACGTGACTGAGCAGCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576192.4 4/1
AGTCTCAGCAGGTGAGAATGTCCACGCGATGAGCTCTTTCTGTGTAGACTTACTATGTACAGAAAGCTTATTTCTTCTGCCCTTTTCCTTCCAACTTGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576192.5 5/1
TGCCTACTGTGATAGGAACACTCAGGACCTGTTGAACTTGAAAGATCTTTAGGCTTAAAGGTTGTACTTGGTACCCTGGAAACACAGGCAGAAAGGACAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576192_2.fastq <==
@SRR6576192.1 1/2
GCCATTTACTCTCTGTCCCTGCCTCAGTATTTCCTGTGTAAACCGTTACAACTTTCTAACAGAACTGTATCTTTCCCTAAGCTGCTCTGCCAAGTACACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576192.2 2/2
AATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF-
@SRR6576192.3 3/2
GAAGAATATGAAACAAATCAATAATATTTCATGAAGAGTTCTTATGGGGGTTGGGGAGGAAAATATAAATGTTAAACATGAATGATGGCCGGGGTGGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFF
@SRR6576192.4 4/2
AGATGTAAATGCAAGGACAGCACAGACCAAACTACCCGCTCATTAGTTCAAATCCAGCATGACTCTCCGGCTGAACCCAGAGCCCCATGAACTTGGGAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576192.5 5/2
GGTTTAAGGGCAGGGCAATTAAGGAGAGAAGCCCTCCACTATCCTTGCTGGCTCCCCAACAGGATCCCAGCTGGTATACTAAGGCTTTCCAAGGGGACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576192_1.fastq

Printing command:
fastqc --outdir SRR6576192_1.fastq

Analysis complete for SRR6576192_1.fastq

Processing SRR6576192_2.fastq

Printing command:
fastqc --outdir SRR6576192_2.fastq

Analysis complete for SRR6576192_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 134M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 39 root   root       52K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:41 SRR6576192_1.fastq
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:41 SRR6576192_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:50 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================