-----------------------
Start of variable list:
-----------------------
Sample_ID:
H2-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-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791239
Current job name : Step_02_H2-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/8791239.1.linga

Loading required modules...


List files in scratch directory:

total 117M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:46 SRR6576123_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  61M Oct 12 19:46 SRR6576123_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576123_1.fastq <==
@SRR6576123.1 1/1
CNTTGATATTCTCTGCATCCTATTTAGGGCTATTGATATTTAACAAATATCCAGCAAAGGTTTTTCCAGGAGATGTTGGAACTCTACCAATTGGAGCTTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576123.2 2/1
CCAATGCTCATTGGATTGGCCTCGGTGCCTCCTGCTTTCCAGCTCTGCTTCATTCCTTCCTGAAAATCAAATGCCTGGCTCCAGCTGGGACATCTTCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576123.3 3/1
TAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAAATAATAACGGCCATGCACCACCACCCACGGAATCGA
+
FFFFFFFFFF-FFF8FFF8FFFFFFFFF8FFFFFF-8FFFF-F-FFFFFFFFFFFFFFF--FFF-FFF-FFFF-FFFF-FFF-F-FF-F-F-FFF-F-FF
@SRR6576123.4 4/1
CTTCTAAGAAGTCCATATACACTTTAGTAATTCTTAGGAGCTCTGGTGTAGACAGGTCAGGATGTCTCCTGGAGTATTCATAAATAAACTCAGCAAAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576123.5 5/1
GGGGAATGGCATACTATTATCCTGGCTTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACCTTTTCTGGAGCAAATCCATGTCTTGGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576123_2.fastq <==
@SRR6576123.1 1/2
NATAAGGCATCATTATAACTAAAAATGGGATATATTCCTTATAAACTACTGCTAAGACAGCTAAGAAAGCTCCAATTGGTAGAGTTCCAACATCTCCTGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFF-FFFFFFFFFFFFF8
@SRR6576123.2 2/2
NTGTTTGTTCATAGAACCTTATGAAATTATGAGGAGGCAAAAGAACTGGATAAAAGTCAGTGTTTCCAGTGTGGAAAGCAGTGAATTAAAGCCTCAGGGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576123.3 3/2
NTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTATCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCA
+
#FFFFFFFFFFFFF8FF-FFFF-FFFFFFFFFFF-FFFFFFFFF-FF--F-FFFF-FF-F-F---FFF-FFFFFFFFFFFFFF-FFFFFFFFFF8FFFFF
@SRR6576123.4 4/2
NCTCTATATGTATGAGGTTGCCAGAAGGAACCCCTTTGTCTTCGCCCCCGTTCTTCTAGCCTTGGCTGCTTGGTTTGAGGAGTCAGCGACCACATGTTGT
+
#FFFFFFF-FF-FFF-FFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFF-F-FFFFFFFF-FFFFFF8FF-FF-FFF-F8F-F8F-FF
@SRR6576123.5 5/2
CTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAGGTCTAAAGTTGCCATTATCTTCTATCTTTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6576123_1.fastq

Printing command:
fastqc --outdir SRR6576123_1.fastq

Analysis complete for SRR6576123_1.fastq

Processing SRR6576123_2.fastq

Printing command:
fastqc --outdir SRR6576123_2.fastq

Analysis complete for SRR6576123_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 647M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 80 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 H2-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 324M Oct 12 19:46 SRR6576123_1.fastq
-rw-r--r--   1 kkarri waxmanlab 324M Oct 12 19:46 SRR6576123_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:06 EDT 2018
0 hours, 0 minutes and 55 seconds elapsed.
==========================================================