-----------------------
Start of variable list:
-----------------------
Sample_ID:
F4-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 19:46:08 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791162
Current job name : Step_02_F4-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/8791162.1.linga

Loading required modules...


List files in scratch directory:

total 117M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:46 SRR6576075_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:46 SRR6576075_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576075_1.fastq <==
@SRR6576075.1 1/1
CAATGTTTGTGCTTGGGCAGTAGAAAGAAAGGCTGGGAGAGCATTTGTGAAGCTACCTAGGCTGCGTAAGTTAAGAAAGAGCATCAAGGAGATCAAAATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFF
@SRR6576075.2 2/1
CTCTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--F
@SRR6576075.3 3/1
GTATCAACGCAGAGTACATGGGAGCTGCTCTAACTAGAGCAAAGAGACAGGACGAAGCTAGTCCGAAGGGGTTGCGACAACCTCAGCAATGTCGAGAAGC
+
-8F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFFFFFFFF--FFFFFFFF-FFFFFFF-FFFFFFFFFFFFFF-FF-FF-FFF-FFFFFFF
@SRR6576075.4 4/1
TCATTACCTTGTCCACAGCATCTGCATCCTTCTGGACATCCAGGAAGCCAGAAAGTTCAGTTTGTAGCAGGTCTTTCAGTTCTTTCTTGCTCAGCTTATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576075.5 5/1
TGCATATGCCGTACCTAAGGTTCTTAAATATGCAGGACTGAAAAAAGAAGACATTGCCATGTGGGAAGTAAATGAAGCATTCAGTGTGGTTGTGCTAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576075_2.fastq <==
@SRR6576075.1 1/2
NGTCATGGACATGGTCATGGTAAGCATACAAATAAAGACAAAAACAGTGTAGAGCAGACTACCCAGAGAACAGAGTCTTTGGCAAGCTCTTCTGAATACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFF-FFFF8---FFFFFFFFFF-FFFFFF
@SRR6576075.2 2/2
TTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576075.3 3/2
TCTCAGAAGGCTTACTGCTGCCAAGATGCTCCTGCCCATGTTTGTTGTGGTGTTAGTGGTGGCAATGAGCCTCTGAGGGCTCCGCAGTTTTATTGGCAGT
+
FF-F--FFFFF-FFFFF-FFFFFFFFFFF-FF-FFF---FFFFFFFF-F-F----F-F---FF-F-FF---FFFFFF-F-FFF-FFFFF-FFFF--FF-F
@SRR6576075.4 4/2
ACGCAGAGTACATGGGGAGGTCTCCTCACACCGGTCCAGTGGCCACATTTGCAGCGTGCCCTTCTGTCGAGAATCTGTTCCGACGTCAGGCCGAGGCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576075.5 5/2
AGCTTATGCTGAATATAACCTGGCCCAAGGGAGTCACATTTACTTCAGCCGGTCACATGGAACTGTCTCCTAAAACAGGTTGTCTACAGCTTCTCAATCA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576075_1.fastq

Printing command:
fastqc --outdir SRR6576075_1.fastq

Analysis complete for SRR6576075_1.fastq

Processing SRR6576075_2.fastq

Printing command:
fastqc --outdir SRR6576075_2.fastq

Analysis complete for SRR6576075_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 649M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 74 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 F4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 325M Oct 12 19:46 SRR6576075_1.fastq
-rw-r--r--   1 kkarri waxmanlab 325M Oct 12 19:46 SRR6576075_2.fastq
==========================================================
Finished on : Fri Oct 12 19:47:01 EDT 2018
0 hours, 0 minutes and 53 seconds elapsed.
==========================================================