-----------------------
Start of variable list:
-----------------------
Sample_ID:
O14-MAA000377-3_9_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 19:46:09 EDT 2018
Running on node : scc-wh2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791295
Current job name : Step_02_O14-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791295.1.w

Loading required modules...


List files in scratch directory:

total 49M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 32 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:46 SRR6577002_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  25M Oct 12 19:46 SRR6577002_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577002_1.fastq <==
@SRR6577002.1 1/1
CTGCATATGGAAAGAAGCAGTGTACCAATCTCTTTCCTAGAACAATTAGAAGAAGATATGTAGTCACCCCCTTTGTGAGAAGAGGAGGTGAATGTGATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6577002.2 2/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFF-FF-FF-FFFF-FFFFFFFFFFFFFFFFF
@SRR6577002.3 3/1
TCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATA
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8F8F8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFF-FF
@SRR6577002.4 4/1
AGTCTTCACCCTAGGCTCCACAACATTCAGGGCTGTCCAATAAATACTGCTATTTTTTAATATTGCATGGCTTGACAGGGCACTCCAGGCCACCACTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577002.5 5/1
GTAGACACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577002_2.fastq <==
@SRR6577002.1 1/2
NTATTACTTCTACCTACTTGATGATGATTGTAAAATGCAAAGGATTTATCTCCTTGATTACATTCAGAGTATTTCATTTCCAAATGAGTTCTTCGGTGTA
+
#FFFFFFFFFFFFF8FFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-
@SRR6577002.2 2/2
NTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTC
+
#FF-F8FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6577002.3 3/2
NTACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTA
+
#FFFFFF8FFF8FFFFFFFFFF8FF8FFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFF-8FFFFFFFFFF8
@SRR6577002.4 4/2
GACAATTCATACACCCACACAAAGGAAGTGGAGAATTGAAGCAATCACACGAGTAATGCATCCTTTGTGCACCCATCCACATGAGCACGCGTCACCAAAA
+
FFFFFFFFFFFFF8FFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8FFF-F-F
@SRR6577002.5 5/2
GAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--8FFFFFFFFFFF

Starting FASTQC command


Processing SRR6577002_1.fastq

Printing command:
fastqc --outdir SRR6577002_1.fastq

Analysis complete for SRR6577002_1.fastq

Processing SRR6577002_2.fastq

Printing command:
fastqc --outdir SRR6577002_2.fastq

Analysis complete for SRR6577002_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 269M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 32 root   root       72K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 135M Oct 12 19:46 SRR6577002_1.fastq
-rw-r--r--   1 kkarri waxmanlab 135M Oct 12 19:46 SRR6577002_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:24 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================