-----------------------
Start of variable list:
-----------------------
Sample_ID:
E8-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 19:46:10 EDT 2018
Running on node : scc-yb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791322
Current job name : Step_02_E8-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/8791322.1.y

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 E8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:46 SRR6576279_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576279_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576279_1.fastq <==
@SRR6576279.1 1/1
CTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCA
+
-F-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFF-FFF--FFF--FF--FF-FFF-F-FF-FF-FF
@SRR6576279.2 2/1
CAGACTACCCAGATGCTTACACCACATGAAACACTGTCTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCATGATCTTTATAATTTGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576279.3 3/1
GAAGTGATTCACATTGAGTTCCATTGGAATTCATCTTAATCAGACCTGTGTGAATAAAAATACAAGAACTGCTTATAGGAGACCAGTTGATCTTGGGAAA
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576279.4 4/1
GAACCCATAGTTCGGTTTTATTCAGAGTAATGGGGGGAAAAGGAAACTTCTGCTCACAGAAGAAACTCAGCCACAGGTCTGATCTGGACTGGAACTACAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576279.5 5/1
CACCAATTTCCTCACAATAAATCAATGATGACGAGACGTAATTCGTGAAGGAACCAACCAAGGCCACCACACTCCTATAGTACAAAAAGGACTACGATAT
+
FFFFF-----FF-FF-FFF8FF8FFF8FF8FFFFFF8F8F--8FFFFF--FFFFF-F-FFFFF-FFFFFFFF-F-FF--FF-FFFF-FFFF-FFFFF-FF

==> SRR6576279_2.fastq <==
@SRR6576279.1 1/2
NTCAATCTGTCAATCCTGTCCGTGTCCGGGCGGGGTGAGGTTTCCCGTGTGGGGTCAAAGTAAGCCGCAGGCTCCTCTCCGGGTGGTGCCCTGCCGTCAT
+
#FFF-FFFF88F888-FFF8FFFFFF-FFFF-F-FFFFFFF-F-FFF-F--FFFF-FFF-F-FFF-F--F-F-FF----8F-F-FF-FFF-F-F-FFFF-
@SRR6576279.2 2/2
GTGTGATATGGTGGAGGGCAGCCATGAAGTCATTCTAAATTTGTTGAAGCATACGATACTGATATTACTTCTCGTTTTGAAGCAAAGGCCTCTCAAATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576279.3 3/2
GTGTGAATGAAGGAACTTAAGAAAGATCAGGACAGGCACAGCTCACTAGTCGCTCCTGAATGCCTCGTGACACTGGGAACATCCTCTCAAGGGTTAAACA
+
FFFF-FFFFFF-FF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFF-FFFFFFFFF-FFFFF-FFF-FFFFF--FFFF8FF
@SRR6576279.4 4/2
GTTCTGATGGAGAGATATTTGAAGTTGATGTAGAAATTGCCAAACAATCTGTGACTATCAAGACCATGCTGGAAGATTTGGGAATGGATGATTAAGGAGA
+
FFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFF8FFFFFFF-FF-FFF8
@SRR6576279.5 5/2
GTAGGCAAACAAAAAGGAATTTATATCCAATAAATACATGGAGTCGATGGAATCCAGTAGACATGAAGAATGTAGAACCATAGATACAATCTGAAAAGGA
+
FFF-FFFFFFFF8FF-8FF88F-8--FF-F-FF-FFFFFFF-----FF-FFF-F-FFFFFFFF-F--FFFF-FF-FFF-FFFFFFF--F-F--F8F---F

Starting FASTQC command


Processing SRR6576279_1.fastq

Printing command:
fastqc --outdir SRR6576279_1.fastq

Analysis complete for SRR6576279_1.fastq

Processing SRR6576279_2.fastq

Printing command:
fastqc --outdir SRR6576279_2.fastq

Analysis complete for SRR6576279_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 136M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 E8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  68M Oct 12 19:46 SRR6576279_1.fastq
-rw-r--r--   1 kkarri waxmanlab  68M Oct 12 19:46 SRR6576279_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:22 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================