-----------------------
Start of variable list:
-----------------------
Sample_ID:
H17-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 19:46:10 EDT 2018
Running on node : scc-yb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791328
Current job name : Step_02_H17-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/8791328.1.y

Loading required modules...


List files in scratch directory:

total 44M
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 H17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:46 SRR6576303_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:46 SRR6576303_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576303_1.fastq <==
@SRR6576303.1 1/1
GCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576303.2 2/1
CACAGGGTGCTGCCTCAGCGCCTCTGTGCTTCTGCCTGTTCCAGAAGCTGTCAGGTTCTCTGGCGCACCCTCTCACCTGTTCAGACTAATTTCCTAAGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576303.3 3/1
GTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576303.4 4/1
GTTACAGGCAGTTGTAAGTTGCATGATATGGATGCTGGGATCTGAACTCTGGTTTTCTGGAAGAGTAGCAACCAGCTCATTTGAAAGAACAACAAATAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576303.5 5/1
GGCTGCACTGCGGGCGCAATTGCTTTGGCATGAGCCGGAGCGGTTACACCCTCGTGAGGAAGGACAGCGAGGAAGAGGTGTCTCTTCTGGGCAACCAGGA
+
FF-FFF8FF88FFF8FFF888FFFFFFFFFFF8FFFFFFFFFF8-FF8F-FFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFF-

==> SRR6576303_2.fastq <==
@SRR6576303.1 1/2
GGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576303.2 2/2
GTGTGGGCCGGGGACAGCCGGCCACCTTCCGGACCAGAGGACAGGTGCCCACCCGGCTGGGGAGGCGGCCTAAGCCACAGCAGCAGCGGTCGCCATCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576303.3 3/2
GGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FFFF
@SRR6576303.4 4/2
CCCTTACACTATACTATGCTTAGAATAAAAGTCTTAAAAGTTGTTTAGAGACAAACTCAGTCACTGTAATGACCAAGGTTACTGAAACACTTATTTTAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576303.5 5/2
CAATCAACGAGGGTGGAACGTTCCCCTGGTAAGTTCTGACCGGAGTGAGTGAGTGAATTCTGTAACATGATAGTCCTCCGTTGATCAGAGCGGGCTTGCT
+
F-FFFFFFF8FFFFFFFFF8F8FFFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFF-F-FFFFFFFF-FFFFFFFF-FF---FFFFFF8-FFFFFFFFF-F

Starting FASTQC command


Processing SRR6576303_1.fastq

Printing command:
fastqc --outdir SRR6576303_1.fastq

Analysis complete for SRR6576303_1.fastq

Processing SRR6576303_2.fastq

Printing command:
fastqc --outdir SRR6576303_2.fastq

Analysis complete for SRR6576303_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 225M
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 H17-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 113M Oct 12 19:46 SRR6576303_1.fastq
-rw-r--r--   1 kkarri waxmanlab 113M Oct 12 19:46 SRR6576303_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:25 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================