-----------------------
Start of variable list:
-----------------------
Sample_ID:
E8-MAA100040-3_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 19:44:32 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791130
Current job name : Step_02_E8-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791130.1.linga

Loading required modules...


List files in scratch directory:

total 59M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  30M Oct 12 19:44 SRR6575213_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  29M Oct 12 19:44 SRR6575213_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575213_1.fastq <==
@SRR6575213.1 1/1
CTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAG
+
-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575213.2 2/1
CTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFF-FFFF
@SRR6575213.3 3/1
CTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCAATTACAGGGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575213.4 4/1
GCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGTCAAATAGCTCC
+
--FFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-F-FFF-FF-FFFF-FFFFFFFFFFF-FFFF--FFFFF
@SRR6575213.5 5/1
AGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAG
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF--FFFFF-FFFFF--

==> SRR6575213_2.fastq <==
@SRR6575213.1 1/2
CCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFF
@SRR6575213.2 2/2
CCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCAC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FFFF-FFFFFFF
@SRR6575213.3 3/2
CCATGGTAGGCACGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6575213.4 4/2
TCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAA
+
-FFFFFFFFFFFFFFFF-FFFFFFFFF--FFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFF
@SRR6575213.5 5/2
CCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FF-FFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFF-FFFFFF-FFFFFF

Starting FASTQC command


Processing SRR6575213_1.fastq

Printing command:
fastqc --outdir SRR6575213_1.fastq

Analysis complete for SRR6575213_1.fastq

Processing SRR6575213_2.fastq

Printing command:
fastqc --outdir SRR6575213_2.fastq

Analysis complete for SRR6575213_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 315M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 158M Oct 12 19:44 SRR6575213_1.fastq
-rw-r--r--    1 kkarri waxmanlab 158M Oct 12 19:44 SRR6575213_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:07 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================