-----------------------
Start of variable list:
-----------------------
Sample_ID:
F19-MAA000377-3_9_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 19:44:29 EDT 2018
Running on node : scc-ye3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791146
Current job name : Step_02_F19-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791146.1.y

Loading required modules...


List files in scratch directory:

total 38M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F19-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:44 SRR6576170_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:44 SRR6576170_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576170_1.fastq <==
@SRR6576170.1 1/1
GGGATGCTGTATGGATAGGAAGGGATGATGCTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCAATCTTCATTCTAGGGCCTGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.2 2/1
GAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.3 3/1
TGTCTGCCAACTTCTTCTGAACCAGCTGGTTCCTGGCCAAGGGGACTCCAAACTGGATCCTGTCTAGGGCATACTGCCGGGCTGTGTGCAAACAGAACTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.4 4/1
AGCCTGGAGAGGAACCTCAGCATCCCAGCCCCCCCTGAGCCTGGCACATAAGCTCAGAGCCCTGTATCTCCCAGGAGGAAGTGTTCCCCAGAAACCCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFF
@SRR6576170.5 5/1
ACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576170_2.fastq <==
@SRR6576170.1 1/2
GTCTTGGAGAATTCCTTAGCTTTTAAACTCCATACTGTATGATGGATTCAATACATTTACTCTACTGAAGACAGAATATGATAATTATATTATGTTTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.2 2/2
TCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGG
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-FFFF-FFFFFFFFFFFF
@SRR6576170.3 3/2
ACTCCCCTGTGGCTGACCTATTTATAGTGTGGGCTCGGTGTGAGGATAACTGTATTCGGGGCTTCATACTGGAGAAGGGTATGCGGGGCCTCTCAGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.4 4/2
CCTGTGCCCAGGGGAGAGAATCTGGAGAGGGAGGGGACTTGTGGAGAATAAATGGTTGTTTATGGCCTTCTGGGGTTTCCAGTGTGGGCTCTCTCACCTC
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576170.5 5/2
CTCAGCTAAGAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTAACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFFFFFF

Starting FASTQC command


Processing SRR6576170_1.fastq

Printing command:
fastqc --outdir SRR6576170_1.fastq

Analysis complete for SRR6576170_1.fastq

Processing SRR6576170_2.fastq

Printing command:
fastqc --outdir SRR6576170_2.fastq

Analysis complete for SRR6576170_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 206M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F19-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 103M Oct 12 19:44 SRR6576170_1.fastq
-rw-r--r--   1 kkarri waxmanlab 103M Oct 12 19:44 SRR6576170_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:42 EDT 2018
0 hours, 0 minutes and 13 seconds elapsed.
==========================================================