-----------------------
Start of variable list:
-----------------------
Sample_ID:
A6-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 19:42:20 EDT 2018
Running on node : scc-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790940
Current job name : Step_02_A6-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/8790940.1.linga

Loading required modules...


List files in scratch directory:

total 59M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6575733_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  31M Oct 12 19:42 SRR6575733_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575733_1.fastq <==
@SRR6575733.1 1/1
GCCTAGGGCTTGCCCTGGCTCTCTGTCTCCTCCCCTATGGAGGAGCAGAGAGCCAAGGCCAAAGCTCTGCTTGTTACAAAGCCCCGGAGTGGTACATAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575733.2 2/1
CCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFF
@SRR6575733.3 3/1
GAGTATACTGTGACATGAAAACAGAAAACGGAGGATGGACAGTCATACAGAACCGTCAGGATGGCAGCGTCGACTTTGGCAGGAAATGGGACCCATACAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFF
@SRR6575733.4 4/1
CCTTCACCGTGGTGGACTCGTCCACGTGGAACTCAGCTTCCTCAGTGTTCTCAGGATCGAATGGCTTCTTCCATTTGCCTTTAAAGAGAATGTAATTTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575733.5 5/1
ACCTTACTTCCCCGAATCAAGCCTAGATTTTGAAGTGTCTGATCCTCCCTGGGCACATGGGGGACACTGGACCAGCAGCACCAGGCTGGCCCACCTTAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF

==> SRR6575733_2.fastq <==
@SRR6575733.1 1/2
CATCTATGCCATCTTCTTCTTGTCTGTACACTGCGATGTGTTCTGACACCTGCTTTTTAAGATGTGAGTGTTTTAATTGGGAAGGAGATCCTTGATGGTT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFFF-FF-FFFF-FFFF-FF--F-F-F-FF-FFFFF--FFFF8F-FFFFFFFFF8FF8
@SRR6575733.2 2/2
TCCCCGCCCCTTGCCTCTCGGCGCCCACTCGATGCTCTTAGCTGAGTGTCCAGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAG
+
FFFFFFFFFFFFFFFFFF-FFFFFF--FFFF-F--F-FFFF-FFFFFFFFF---FFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFF-FFFFF8FF8F
@SRR6575733.3 3/2
GACTATTGCTGTGGGAAGAAGGGCCTGATCTTCATAGACATCCTCCTCATTGAGTACCACGATCCCTTCCATTTCATCCACACCACACCATCATCTGTGC
+
F-FFFFFFFFFFFFFF8FFFFFF8FF-FF-FF-FFFFFFFFFFFFFF--FF-FFFFFFFFFFFFFF-F-FF-FFFFFFFF--F-FFFFFFF8--8FF8F-
@SRR6575733.4 4/2
GGACCAAGACACAGTTTTCGCCCTGGCAAATTACATTCTCTTTAAAGGCAAATGGAAGAAGCCATTCGATCCTGAGAACACTGAGGAAGCTGAGTTCCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FFFFF
@SRR6575733.5 5/2
CCTACCAGCTGACCCACCTGCATCTGTGGTGGTGGGACCTGTGGTGGTTCCACGAGGACTTTCAGACCACCGAACTTACCACGACCTACGCCACGCCTTC
+
FFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF

Starting FASTQC command


Processing SRR6575733_1.fastq

Printing command:
fastqc --outdir SRR6575733_1.fastq

Analysis complete for SRR6575733_1.fastq

Processing SRR6575733_2.fastq

Printing command:
fastqc --outdir SRR6575733_2.fastq

Analysis complete for SRR6575733_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 318M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 50 root   root      112K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 159M Oct 12 19:42 SRR6575733_1.fastq
-rw-r--r--   1 kkarri waxmanlab 159M Oct 12 19:42 SRR6575733_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:58 EDT 2018
0 hours, 0 minutes and 39 seconds elapsed.
==========================================================