-----------------------
Start of variable list:
-----------------------
Sample_ID:
G9-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 19:41:27 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790793
Current job name : Step_02_G9-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/8790793.1.linga

Loading required modules...


List files in scratch directory:

total 33M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576367_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576367_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576367_1.fastq <==
@SRR6576367.1 1/1
GNCACTGCCTGCCCAGTGACTAAAGTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAATTAGGGACTAGCATGAACG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576367.2 2/1
TGCTTTAGGAATAACCCCTCCCCCTCGAGATTGTCCTCTCTGTGCACATGCCTCCCACTAGAGACATGAGCACACAGGCACATTTTTAAAGAATATTGGT
+
88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576367.3 3/1
GTGAGGACCGACTTCCAGGTCGGCCCCTGTCCTTTGCCCGCTGTGACACTGGGCAGAGTGAAGATCTTCCAGGCCACCAAAGCCAGTACCACAGCACCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576367.4 4/1
AGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAATCCAACCCGGTGAGCTCCCTCCCGGCTCCGGC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576367.5 5/1
TCAGAAGAGTGTCTGAGAACGTCTATTTCATCCTTTAGAGACTGAGCTTCGTCTGCCAAAGTGGTCAGCTCATCGTTCTGCTGCCGAAGCTCAGAGATTT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF

==> SRR6576367_2.fastq <==
@SRR6576367.1 1/2
NTAAGNTATGTTGATTTTACTTTGACTTGTAAGTCTAGGTTATAATCATTCGGAGGATTTTTTATTCTCCGAGGTCACCCCAACCGAAATTTCAAACTTA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF--FFFF
@SRR6576367.2 2/2
NTTTAGTCGCACAAGAACTTAAGCCTTAAGAAGAGATGAATTTTGATCTACTTACTGTCATCTATCACTCTGGTATCTAGGAGAACGTCTACCTGACAAG
+
#-FFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF--FFFFF-F-FF8--
@SRR6576367.3 3/2
NTCTTCCTGGCCTTCACCATGGTGCTCTATGTTGCCTTCAGGTTCTCTCTGCAGAGGTTCAAGTCTGAAGATGCCCCTAAGATCCACATGGCTCTGAGCA
+
#F-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FF-F-FFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576367.4 4/2
GTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTC
+
FFFFFF-FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFF-FF-FFFF-F-FFFFFFFFFF-FFFFFFFFF
@SRR6576367.5 5/2
GTGCTGTGAACTGTGAGCAGAAGCAAGTGTACATTCAAGCCATTATGATGATGGAGGACTCTGTTCAGCATGTCGTCATGACAGCCATTCAAGAGCTAAT
+
FFFFFFFF-8FFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFF-FFF--F

Starting FASTQC command


Processing SRR6576367_1.fastq

Printing command:
fastqc --outdir SRR6576367_1.fastq

Analysis complete for SRR6576367_1.fastq

Processing SRR6576367_2.fastq

Printing command:
fastqc --outdir SRR6576367_2.fastq

Analysis complete for SRR6576367_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 160M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:41 SRR6576367_1.fastq
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:41 SRR6576367_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:51 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================