-----------------------
Start of variable list:
-----------------------
Sample_ID:
F5-MAA100138-3_56_F-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 19:46:08 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791165
Current job name : Step_02_F5-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791165.1.linga

Loading required modules...


List files in scratch directory:

total 47M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:46 SRR6575864_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:46 SRR6575864_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575864_1.fastq <==
@SRR6575864.1 1/1
CTCCTCCTCCGGATCAGCCATGACCTCTCTGATTCGTCTGAATTATTCCACCGAGGTGGAAGCTGCCGTGAACCGCCTGGGCCTGTTGCACCTGCGGGCC
+
--F8--FFFFFFF-FFFF88FFF8FF8FF8F8FFF-8F8FF-FFFFF--F--FFFF-FFF-FFFF-FFF---F--F-FFF------FF---FFFFFF-FF
@SRR6575864.2 2/1
CTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCA
+
F-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF8FFF--FFFFFF-FFFFFFFFFFFF--FFFFFFFFF-FFF-FFF-FFFFFF-FFFFFF-FF
@SRR6575864.3 3/1
ACGTTCTCTCCTGATGGAAGAGTTTTCCAAGGTGAATATGCCATGAAGGCTGTGGAAAACAGTAGTACAGCTATTGGGATCAGATGTAAAGATGGTGTTG
+
8-FFFFFFFFFFFFFFFFFFF8FFFF8FFF88FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFF-F-FFFFF-FF-F-FF-FFFFFFF-FF
@SRR6575864.4 4/1
TGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTTATTCCGATAACGTACGAGACTCTGGCA
+
8F--F8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFF-FFF-FFFF--FFFF-FFFFFFF-FFFF-FF-FF--FFFFF-F
@SRR6575864.5 5/1
TATCTACACTGAGTGCAAGCCATAATATAGTGATAAGCCGTGTGTCGCAAGTTCTTCATGAAGGTGGCCACAATGTGACCAAACTTCTTTATGAAAGTGC
+
-F8FFFF-FFFFFF8FFFFFFFF8F8F8FF8FFFFFFFFFFFFFFF-FFFFFFF-FFFFFF--F-FFFFFFFF-F-FFF-FFFFFFFFF-F-FFFF--FF

==> SRR6575864_2.fastq <==
@SRR6575864.1 1/2
NCTCCAGGGTGGGTACCAAGCTGCCGAGTGGCTGGAGAGGTTCAGTCAGGTGGAGGTCCCAGGGCGGGCTGGTGCAGAGCTGCGGGGGGAGCCCCGGGGC
+
#8-FFFFF-8FFFFFF8FFFFFFFF-F-F-FF---F-FFFFFFF---FFFFFFFF-FFFFFFFFFFFFF-FF-F-FFFF----FF-FF-FFFFF--F-8-
@SRR6575864.2 2/2
AGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGATCGAAGACGAT
+
F-FFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF--FFF-FFFF-FF--FFFFFFFFFFF-FF-FFFF-FFF-FF--F-FFFF-FF8F
@SRR6575864.3 3/2
TCCTTCATCTGAAGCTTTTCTATCTCTGTCTTTGCAGCCTGCCTGGCTTTGCCAATCGCACAGCCCCAGTAACCATATGAAACACCTGAGGGGTCGATCA
+
8F---FFFFFFFFFFFFF-FFFF8F--FFF-FFFFFF-FFFFFFFFF-FFFFFF--FFFFFF-FF-F-F-FFFF-F-FF-FFFFFFFFF-F8FF8FFFF-
@SRR6575864.4 4/2
CCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFF-FFF8FFFFFFFFFF8FFFF
@SRR6575864.5 5/2
CCCAAAGTCCAAATAGCAAAATTCTAAGGGAAGAAAGGACACAAATCGTTTCACAAGCTTTTCAACAATTTGGAAAGTACAGATAACCAATGAAACAAGA
+
F-FFFFF-FFF-FFF-F-FFF8-8-FFF--FF-FFF--FFFF--FFFF-FFFF-FF--FFF--FF-FFFF---F--F-F-F-F--F-FF--FFF-FFFFF

Starting FASTQC command


Processing SRR6575864_1.fastq

Printing command:
fastqc --outdir SRR6575864_1.fastq

Analysis complete for SRR6575864_1.fastq

Processing SRR6575864_2.fastq

Printing command:
fastqc --outdir SRR6575864_2.fastq

Analysis complete for SRR6575864_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 202M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 74 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:46 SRR6575864_1.fastq
-rw-r--r--   1 kkarri waxmanlab 101M Oct 12 19:46 SRR6575864_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:34 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================