-----------------------
Start of variable list:
-----------------------
Sample_ID:
C2-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-tk2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790743
Current job name : Step_02_C2-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/8790743.1.linga

Loading required modules...


List files in scratch directory:

total 30M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576177_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:41 SRR6576177_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576177_1.fastq <==
@SRR6576177.1 1/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTGTTTTAAAATAAAAAAAAAAAAAGTTTT
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFF-------FFFFF--FFF-FFFF--F--FF-F
@SRR6576177.2 2/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
F--8F8-FFFFFFFFFFFFFFFF8FFFFFFFFFFF-FFFFFFFFFF-F-FFFFFF-FFF-FFFFFFF--FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576177.3 3/1
TGGTACACACGGCATGTGTAATTCTGCTCCTTCCCAAGAGGCACCACCACAGATGCCCACTTCTGGAAGGTTCCATCCCCTGCAGGCCTGGTCTCCACAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576177.4 4/1
GGGTAGTCTGAGTAGCGTCGGGGTATTCCTGAAAGGCCCAGGAAATGGTGAGGGAAGAATGTTATGTTTACTCCTACGAATATGATGGCGAAGTGGGCTT
+
FFFF-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576177.5 5/1
CCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576177_2.fastq <==
@SRR6576177.1 1/2
GTAGTGAACCTTTTGTATGATAGCGATCCTGTTTCAACGTTGTTACACTCAAGCCAAGATTGAATGTCTGACATGAACCGTGAATGATCTTGTCACTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF8F--FFFFF
@SRR6576177.2 2/2
CGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCGTCCTTGGAGGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGACTCGAACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFF-FFFFFFFF-FFFFFFFFFFF-FFFFFFFF
@SRR6576177.3 3/2
CCTGGAGGGCGAGTGCGTGGAGTGGCTCCACAGATACCTGAAGAACGGGAACGCGACGCTGCTGCGCACAGATTCCCCAAAGGCACATGTGACCCATCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576177.4 4/2
GCCTTAGGCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATACATACTATGTAG
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFFFF
@SRR6576177.5 5/2
GGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576177_1.fastq

Printing command:
fastqc --outdir SRR6576177_1.fastq

Analysis complete for SRR6576177_1.fastq

Processing SRR6576177_2.fastq

Printing command:
fastqc --outdir SRR6576177_2.fastq

Analysis complete for SRR6576177_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 151M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 36 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 C2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576177_1.fastq
-rw-r--r--   1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576177_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================