-----------------------
Start of variable list:
-----------------------
Sample_ID:
D6-MAA100138-3_56_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 19:44:30 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791086
Current job name : Step_02_D6-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791086.1.linga

Loading required modules...


List files in scratch directory:

total 108M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 41 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:44 SRR6575812_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:44 SRR6575812_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575812_1.fastq <==
@SRR6575812.1 1/1
ACACAAGGCAGTCTCTGATCTTCAGGAAGTGTACAACACTTGGTGCCCACTCTTCCTAGGTTTCTTGCAGCCTCCACGAGAGTTGGGGTTGACACCTGAG
+
8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFF
@SRR6575812.2 2/1
TNCCAGAAGTCCCGAGTCAATGGGCCCAGCCGTTCCTGCAGCTGACTAACGGTTGAACCCAGAGTGTCCCAGTTTTCCAGGAGATTCAGGTTCAGCTGTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFF-FFFFFFF-
@SRR6575812.3 3/1
GTGTAAATATTTAGGTACAGGCAATCTTCAGAAAATTCAAGATGGATTTTCTCCTTTCTATTGGTTATGAGGTCATTGACCGCCTGTCCTCTAGCTGCAT
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---F-FFFFFFFFFFFFFF-FFFFFFF-FFF
@SRR6575812.4 4/1
GTACAGAGGATGGCTCCCCTTCCAATGAGCTGGTGTCTGGAGGATCTGACAATCGGGTGATTCATTGGGAACTAGAGTATAATCAGGTTTTAAAATCAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFF-F-F--F-FFF-FFFFFF--FFFFFFF
@SRR6575812.5 5/1
GGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCAT
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFF-FF-FFFFFFFFFFFF-FFFFFFFFFFF-FFF

==> SRR6575812_2.fastq <==
@SRR6575812.1 1/2
NACCAGGAAGTGTGCAAGAACTATGCTGAGGCCAAGGATGTCTTCCTGGGCACGTTCTTGTATGAATATTCAAGAAGACACCCTGATTACTCTGTATCCC
+
#FFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFF
@SRR6575812.2 2/2
NATCAACGCAGAGTACATGGGGACACCCAGACTGTCGGAGAGCTCCGGGGAGGTCACCCACACCCTTCAGGATGAAAGCTGTGGTGCTGGCCGTGGCTCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575812.3 3/2
NAGTACATGGGGGACTTGGGAGCCTGTCCATGCAAGATGTTCCTTAGCACTCTGTTCCTGGTGTCTCTAGCAACCTGTGTGATTTGCGGAAATCCCTCTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575812.4 4/2
ACCAAAGGTTGCCCATTCCACGCCTCTTAACCAGTCCTCGTGTCCGCAGAGAGAAAGAGCTTTCTGAAACTGGTCATCCTGTTGAATATATAAGTGAATT
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575812.5 5/2
AGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGG
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575812_1.fastq

Printing command:
fastqc --outdir SRR6575812_1.fastq

Analysis complete for SRR6575812_1.fastq

Processing SRR6575812_2.fastq

Printing command:
fastqc --outdir SRR6575812_2.fastq

Analysis complete for SRR6575812_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 621M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 40 root   root       36K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 D6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 311M Oct 12 19:44 SRR6575812_1.fastq
-rw-r--r--   1 kkarri waxmanlab 311M Oct 12 19:44 SRR6575812_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:03 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================