-----------------------
Start of variable list:
-----------------------
Sample_ID:
K1-MAA000907-3_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 19:46:12 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791272
Current job name : Step_02_K1-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791272.1.linga

Loading required modules...


List files in scratch directory:

total 9.7M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 125 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 K1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 4.6M Oct 12 19:46 SRR6576504_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab 5.0M Oct 12 19:46 SRR6576504_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576504_1.fastq <==
@SRR6576504.1 1/1
AGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576504.2 2/1
GTATTAAGTAGTGGGACTTCTAGAGGGTTAAGTGGTGAAATTCCTGTTGGAGGTCAGCAGCCTCCTAGATCATGTGTTGGTACGAGGCTATAATGATAGA
+
FFF8FFFFFF-FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFFFFFFFFFFFFFFF-FF--F--F--FFFFFFF-F
@SRR6576504.3 3/1
GACTTAATTCTTTTATTTTTCTCATATAAAAACCCTTATGTGGTAGCCACAGCTGGAGCCTGGGTCCTCTGAACAGAGACTCTGGTGTGGGTTTTCACAA
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFF
@SRR6576504.4 4/1
GCCATCAGCGGCGCGCAAGTCGATGGCGCCGAGCTCGGTTCGCAGTCGCTGCGTTTCGCGCCCGGCCCGGTGCGCGCTGGCGAGTACCGCTTCGCAATTT
+
88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576504.5 5/1
ACCTATAACTTCTCTGTTAACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576504_2.fastq <==
@SRR6576504.1 1/2
GTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCA
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFF
@SRR6576504.2 2/2
CACTCCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCAACGTCTCGGAAGTATATTTCTTAGCAGGATTCTTCTGAGCGTTCTATCATTCT
+
FFFF-F-F-FFFFFFFFFF8FFFFFFFFFFF-FFF-FFFFFFF-F-F--FFF-F-FFFFFFF-FF-FF---FF--F--FFFFF-FFFF-FFFFFFFF-8F
@SRR6576504.3 3/2
TCTCATCCCTGCCCCCAGAGGCACTGGCATTGTCTCTGCTCCTGTGCCCAAGAAGCTCCTGATGATGGCCGGTATAGATGACTGCTACACTTCAGCCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6576504.4 4/2
TCACCAGCCCGTGCGCGACCTGCTCGGCGCTCAGCGACTTCTCGCCGAAGGCGGTGAAAACCTCGGTCACGTGCTCGTAGGCCAGCGTGGCAAGCAGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFF-FFFFFF
@SRR6576504.5 5/2
GTTATATAATTTAAGCTCCATAGGGTCTTCTCGTCTTATTATTATATTTCAGCCTCTTCACTGAAAGGTCAATTTCACTGATTAAAGATAAGAGACAGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFF-FFFFFFFFFFF8FFFFFFFF

Starting FASTQC command


Processing SRR6576504_1.fastq

Printing command:
fastqc --outdir SRR6576504_1.fastq

Analysis complete for SRR6576504_1.fastq

Processing SRR6576504_2.fastq

Printing command:
fastqc --outdir SRR6576504_2.fastq

Analysis complete for SRR6576504_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 54M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 121 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 K1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576504_1.fastq
-rw-r--r--    1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576504_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:29 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================