-----------------------
Start of variable list:
-----------------------
Sample_ID:
L11-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 19:46:09 EDT 2018
Running on node : scc-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791276
Current job name : Step_02_L11-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/8791276.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 L11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.8M Oct 12 19:46 SRR6576569_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6576569_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576569_1.fastq <==
@SRR6576569.1 1/1
CTGCTGACCTTCGCCATGAGCTGCACGGCGCACGTGTTCAGCTGCCTGTCGCTGCGCCTGCGCGCCGCCTTCTTCTACCTGGACTACGCTTCCATCAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576569.2 2/1
GCTGTACACAGAGAGCGAGGCGTGGCCGGTGCCTTATGCCGTGGCATGTCCTGAAATGTTTCCAGGGTTGCTGTGTCTTTCAACTCTTGCTTAACTTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576569.3 3/1
GTATTGGAGTCTTTAAAGCTATACTCAAACCCACGTAGATCATTCCAAATAATCTCGAGTTATATAGCCTGCATGCTCCACGTGCTCCACAGCTGGTTAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576569.4 4/1
CCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTC
+
-8FFF8FFFFFFFFFFF8FFFFFFFFFFFFFFFFFF8FFFFFFF-F-8FFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF-FFF-FFFFFFFFFFFFFFF
@SRR6576569.5 5/1
CTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGATGCGTGCATTTATCAGATCA
+
FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6576569_2.fastq <==
@SRR6576569.1 1/2
GTGTGGGGTTCTCGCCTCGCAGGTCGAAGAGCCAGCTCTCTAGCATAATGGGGCAGGCCATGCTGAGCGGCATGACGAAGACGAAGGTGCGCAGGGCGAA
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF--
@SRR6576569.2 2/2
GCCTATGGTCTTCATAAAAGCTCAGCAGCTCTCTTGCTGGGAGATTCGTGATCAGACAATTGGTATTTCTCTTTAAACAATAAAAAGCAATTGCCAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576569.3 3/2
GTGCATTTATAGTGAAACAAACTAGAAATCAAAAGAAATAAGAGCACCCTTGTCAGGGCCTAGCTGTGCATCTGAAGCTGTATGGGTTGTAAAGACTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6576569.4 4/2
GTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTAGCCTCTCGGCGCCCCCTCGCT
+
F-F-FFFFFFFFFFFFFFFFF8FFFFFFFFFF-FFFFFF-FFFFFFF-FFFF-F-FF-F--FFFFF-FF-FFFFFFFF-FFFFF-FF8-FFF--8-FFFF
@SRR6576569.5 5/2
CCCCCGGCCGTCCCTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF8FF

Starting FASTQC command


Processing SRR6576569_1.fastq

Printing command:
fastqc --outdir SRR6576569_1.fastq

Analysis complete for SRR6576569_1.fastq

Processing SRR6576569_2.fastq

Printing command:
fastqc --outdir SRR6576569_2.fastq

Analysis complete for SRR6576569_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 113M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 L11-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:46 SRR6576569_1.fastq
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:46 SRR6576569_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:22 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================