-----------------------
Start of variable list:
-----------------------
Sample_ID:
F4-MAA100039-3_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 19:46:08 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791159
Current job name : Step_02_F4-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791159.1.linga

Loading required modules...


List files in scratch directory:

total 90M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:46 SRR6576922_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:46 SRR6576922_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576922_1.fastq <==
@SRR6576922.1 1/1
GTAGTAGTCAGTCGAATCCATTCAAGGTCGCTTAGTCCAACTTAATGAAGCCTATGTCCTTCGCGTACTGCCGGAAGCACTGGCGGCACATGTTCAGCCC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F--F-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576922.2 2/1
GGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-FFF-FFFFFFFFF-F-F--F-FFFFFFFFFF--FFFFFFFFFFFF-FFFFFFFF
@SRR6576922.3 3/1
GGTAAAGGTTGGGCATCACACTGCAGAAGGAGTGGGTACCAATAAGAAGGTGGCCAAGCGTAATGCTGCTGAGAACATGCTGGAGATCCTGGGGTTCAAA
+
FF8-FFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFF-FF
@SRR6576922.4 4/1
ATGTAAATACAGATCGGCCGGGGCTCTTGGACCTCAAGGGCAAAGCCAAGTGGGACTCGTGGAACAAGCTGAAAGGGACTTCCAAGGAAAGTGCCATGAA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFF-FFFFFFFFF
@SRR6576922.5 5/1
AATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576922_2.fastq <==
@SRR6576922.1 1/2
NATACGGGCTGAACATGTGCCGCCAGTGCTTCCGGCAGTACGCGAAGGACATAGGCTTCATTAAGTTGGACTAAGCGACCTTGAATGGATTCGACTGACT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576922.2 2/2
TGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFF8FF-FF
@SRR6576922.3 3/2
GAAGAGATGTTACTCTTTAAAATGGTCTCGGCTGTGGGCGAGGTGCCCCCGTACAACAACTCTCGGGCTATCATGGCAGTTACCGTTGCCTTGGCAGGAT
+
-FFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F-FFFFFFFFF-FFF8FFFFFFFFFFFFFFFFFFFF
@SRR6576922.4 4/2
AAACTACAGAGGGAGGAGGAGCAGAGGTTAACGCTGGCCCTAATGTATCACAGCCATATCATCTACATTAGAAAAAACCAAGGCATTATGTCCTCACAGG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576922.5 5/2
CATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576922_1.fastq

Printing command:
fastqc --outdir SRR6576922_1.fastq

Analysis complete for SRR6576922_1.fastq

Processing SRR6576922_2.fastq

Printing command:
fastqc --outdir SRR6576922_2.fastq

Analysis complete for SRR6576922_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 505M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 253M Oct 12 19:46 SRR6576922_1.fastq
-rw-r--r--   1 kkarri waxmanlab 253M Oct 12 19:46 SRR6576922_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:51 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================