-----------------------
Start of variable list:
-----------------------
Sample_ID:
B1-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 19:41:26 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790726
Current job name : Step_02_B1-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/8790726.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 117 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 B1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  15M Oct 12 19:41 SRR6575926_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  15M Oct 12 19:41 SRR6575926_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575926_1.fastq <==
@SRR6575926.1 1/1
GTGTACAACTGAAGATAACCAGCATCTTCATATGCTGGTAGCTTACCACTGGAGCTCCCAGTTGCCAAGCCCTTTCTTTATATTAATATTTCAACCATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575926.2 2/1
CAGCCAGACATCTGCTGGAGTGTGTGAGAGCCGACAGCGCTCTGGTTGTAGTAGCCGAGCAGGTTCCTCAGGCTCACTCGGAACCACTGCTCGTGGCCCT
+
F-FFFF-F--F-FFFF-FFFF88F88FFF888F88-F8F8F-8F-FF--FFF-FFFFFFFF-F-FF-FFFF-FFFFFFFFFF-F-F--FFFF-FFFFF-F
@SRR6575926.3 3/1
GAGGAAAGGGCTCCCTGCATGGTGACAAGCCTCTTACCATAAACAGGATTTTCAAAGGGACAGAACAGGGTGAGATGGTGCAGCCAGGGGATGAGATCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575926.4 4/1
CATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575926.5 5/1
CATATAGGATATGAGATTGGCTTGAAACCAATTTTAGGGGGTTCGATTCCTTCCTTTCTTATTTTACTTTTACATAGGTTGGTTCCTCGAATGTGTGATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFF

==> SRR6575926_2.fastq <==
@SRR6575926.1 1/2
CTCTTACGATGTCTATTTGTTCCTGCTGCACTTAACTGTCAGTGAGTCTCTCTCCCAGCTCTGGTTTGGTTGATTTAAACTTTCGTTTTTATGTTTGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575926.2 2/2
GGTATCAACGCAGAGTACATGGGAGACACCCGGGATCCCAGATGGGGGCTATGGCTCCGCGCACGCTGCTCCTGCTGCTGGCGGCCGCCCTGGCCCCGAC
+
---FFFFFF8FFFFFFF-FFFFFF-FFFFF--FFF-F-FFFFFFFFFFF-FFF-F-FFFFFFF--FFFFFFFF--FFF---FFFFFF--FFF---FFFF-
@SRR6575926.3 3/2
GCAGTGACCCTTCACAGGACCCCAGCCCAGCCTTGACCTGCTCGAGCTGATAGTAAGGAGCTCCCCTCCAAGACATGAGATGCATGAGAGAAAAAAAAAA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF8FF
@SRR6575926.4 4/2
GTGATATGGTGGAGGGCGGCCATGAAGTCATTCTAAATTTGTTGAAGCATACGATACTGATATTACTACTTGTTTTGAAGCAAAGGCCTCTCAAATAATA
+
FF-F-FFFFFFFFFFFFFFFFF-8FFF-FFFFF-FFFF-FFFFF-FFF-FFFFFF-F--F-FFF-FF-F---FF-F-FF-F-FF8FFF-FFFFF8--F8F
@SRR6575926.5 5/2
ATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTCACCCT
+
FFFFFFFFFFFFFFFFFFFFF8-8-FFFFF-FFFFFFFFFFFFF-FFF-FFF-FFF-FFFFFFFF-FF-FFFFFFFF-FFFFFFFFFFFFF-FFFF-FF8

Starting FASTQC command


Processing SRR6575926_1.fastq

Printing command:
fastqc --outdir SRR6575926_1.fastq

Analysis complete for SRR6575926_1.fastq

Processing SRR6575926_2.fastq

Printing command:
fastqc --outdir SRR6575926_2.fastq

Analysis complete for SRR6575926_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 142M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 B1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  71M Oct 12 19:41 SRR6575926_1.fastq
-rw-r--r--    1 kkarri waxmanlab  71M Oct 12 19:41 SRR6575926_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:52 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================