-----------------------
Start of variable list:
-----------------------
Sample_ID:
H7-MAA100140-3_57_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 19:46:11 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791252
Current job name : Step_02_H7-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791252.1.linga

Loading required modules...


List files in scratch directory:

total 34M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 101 root   root      180K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  16M Oct 12 19:46 SRR6576134_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  18M Oct 12 19:46 SRR6576134_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576134_1.fastq <==
@SRR6576134.1 1/1
CTTCCAAAGAGCCTTCCAGTTGGCAACACAGTCTTTGATCTGAATAAGTTGGCCAACATGATTGCCGATGTTGACCTGCCTAGTGTCACCCTGCCAACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576134.2 2/1
GTCCAATTCCAGTCTATCCACATGTTACCTAGGATACCTCATCAAGAATCAAAGACTTCTTTAAATTTCTCTTTGATATACCCATGACAATTTTTCATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576134.3 3/1
TCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCATTGGCAACAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATTTTTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FF
@SRR6576134.4 4/1
GTTAAGGCTGATTATATTAAATTTCTAACCCAAATACAAAAGAATAGAGCCTACTGATGCTAGTCTTTTAGCTGAATTTTCCCTGATTCCTAATTTCTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576134.5 5/1
GTATCAACGCAGAGTACATGGGGCTTCCATGATGGCCGCGTTGGCCGCGTTCAGCCGGCGCTCCGCAAGCCCCTTGGCGCGCCGGTCGGCAGCCTCCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576134_2.fastq <==
@SRR6576134.1 1/2
GTAAAAGTGGGGACCTGGACCTCTCGAGATGGCAGATGGAATCCCACAGACTTGAAGTTGAGGGCTGGTGTCCTCACACTCTCTGGCATCTTGAGGTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576134.2 2/2
GGTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FF
@SRR6576134.3 3/2
CAGTGGAAAGCTGGGTGTTGATTTCATGAATGCGATTTCTGATATGGCGGCGGTCGGTTTCCAGTTTCGTTTCCCCGGGACCTCTTGCCCCAATTCCTCC
+
FF-FFFFFFFFFF8F-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-F-FFFFFFFFFFFFFFFFFFFFFF8
@SRR6576134.4 4/2
GGTTTTAATGCGTGAAAGGAGCAGAGAAATTAGGAATCAGGGAAAATTCAGCTAAAAGACTAGCATCAGTAGGCTCTATTCTTTTGTATTTGGGTTAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFF-FFFFFFFFFFF
@SRR6576134.5 5/2
GTGCGCGACGAGCGCGGCTTCGTCGAAGCATTGAATGAAGGCGGCTTCTCGCTGATCCTGTCCGACTACGAGCTGCCGGGGTTCTCGGGCGCGCATGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576134_1.fastq

Printing command:
fastqc --outdir SRR6576134_1.fastq

Analysis complete for SRR6576134_1.fastq

Processing SRR6576134_2.fastq

Printing command:
fastqc --outdir SRR6576134_2.fastq

Analysis complete for SRR6576134_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 203M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 90 root   root      180K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 102M Oct 12 19:46 SRR6576134_1.fastq
-rw-r--r--   1 kkarri waxmanlab 102M Oct 12 19:46 SRR6576134_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:38 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================