-----------------------
Start of variable list:
-----------------------
Sample_ID:
E3-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-tk4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791115
Current job name : Step_02_E3-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/8791115.1.linga

Loading required modules...


List files in scratch directory:

total 101M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:44 SRR6575833_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:44 SRR6575833_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575833_1.fastq <==
@SRR6575833.1 1/1
CCCCGCTCCTCGCCACACACACACCGAGAGGATGAGGCTCACCGTGGGTGCCCTGCTGGCCTGCGCTGCCCTGGGGCTGTGTCTGGCTGTCCCTGACAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6575833.2 2/1
GATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575833.3 3/1
GTCCAGTCATGACCTCGATCCATCGCGTATAGGGACGCCCCCTGCTCGCGTTACTGCCAAGCGAGCGTGGTGTGGTGCCCCCGACCTACAACTTGCGCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575833.4 4/1
GTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCC
+
FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFFFFFF---FFFFFFFF-FFFFFF-FFFFFFFFF-F-FFFFFFF
@SRR6575833.5 5/1
GCAGCAACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACT
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFF

==> SRR6575833_2.fastq <==
@SRR6575833.1 1/2
NCGTAGTAGTAGGTCTGTGGATGTTCCACTGATCCATAAAACTCCGCCGCCACGGGCTTCAGGTTGTTCGGAGTCAGGCCGGCATCGTACACCCAACCCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575833.2 2/2
GCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACC
+
-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6575833.3 3/2
GAGTCCCTCAGCGTGACGCAGTAAACTAGTAGCATCCCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTTGTGCGCCGGCAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFF-FFFFFFF-FFFF-F-8
@SRR6575833.4 4/2
GATCCAACTACGAGCTTTTTAACTGCAGCAACTTTAATATACGCTATTGGAGCTGGAATTACCCCGGCTGATGGCACCAGACATGCCCTCCAATGGATCC
+
FFFFFFFFFFFFF8FFFF-8FFFFFFFFFFFFF-FFFFFFFFFFFF-FF-FFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF-FFF-FFFFFFFF-8FFF
@SRR6575833.5 5/2
CCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6575833_1.fastq

Printing command:
fastqc --outdir SRR6575833_1.fastq

Analysis complete for SRR6575833_1.fastq

Processing SRR6575833_2.fastq

Printing command:
fastqc --outdir SRR6575833_2.fastq

Analysis complete for SRR6575833_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 572M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 38 root   root       52K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 E3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 286M Oct 12 19:44 SRR6575833_1.fastq
-rw-r--r--   1 kkarri waxmanlab 286M Oct 12 19:44 SRR6575833_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:02 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================