-----------------------
Start of variable list:
-----------------------
Sample_ID:
A6-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 19:42:20 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790941
Current job name : Step_02_A6-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/8790941.1.linga

Loading required modules...


List files in scratch directory:

total 85M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:42 SRR6575946_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  41M Oct 12 19:42 SRR6575946_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575946_1.fastq <==
@SRR6575946.1 1/1
GACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTG
+
FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6575946.2 2/1
GTACAAGAAGCTGGCTTTGAAGAATCAAGATAAAAATAATGTCTTCTCCCCACATAGCATCTCAGCTCCCATGGCCCTCGTGTCCCTGGGAGCAAAGGGC
+
F-FFFFFFFFFFFFF--FFFFFFF8FFFFFFFFFFFFF8F--F-FFFFFFFFF-FFFF-FFFFFFFF-FF-FFFF-FFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575946.3 3/1
ATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTC
+
FFF8-FFFFFFFFFFFFFFF8FFF8F88FFFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFF-F-FFFFFFFFFFFF-FF
@SRR6575946.4 4/1
CTCTGAGGCATCTTCCTCAAGGCACATCATCTTCAGGTCAGCAGGGGGCACCTTCCTGTTCTTCTGTGCAATTTGCTCCATTATCCTTACCGCTTGAGTG
+
FF-FF-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFF-FFF-FFF
@SRR6575946.5 5/1
GCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCG
+
FF8FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFF-FFFF-FFFF--FFFFFFFFFFFFFFFFF-FFFFFFF

==> SRR6575946_2.fastq <==
@SRR6575946.1 1/2
GTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGATTCAATACATTTACTA
+
8FFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575946.2 2/2
GTCCTGGGGGTCAAAGGATATCTTCCATTTGCCTTTAAAGTAGATGTAATTCACCAGCACCATCAATGTCCCATCATCCAGTTCTGAGATCTGTTTCTTG
+
-FFFFFFFFF8FFFFFF-FF8FFFFFFFFFFFFFF-F-FFFFFFFFFF--FFFFFFFFFF-FFFFF-FFFFFFFFFFFF----FF-FFFFF-FFFFFFF8
@SRR6575946.3 3/2
ATCCTATAGAAGAGACAGTGTTTCATGTGGTGTAAGCATCTGGGTAGTCTGAGTAGCGTCGTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FFF
@SRR6575946.4 4/2
GAACTACACCGTGCCGGGCCTGGGGTCTGCGGGTGAGGCCTCCTTCCTCAGCCTATGCATGAAGTATGAGGTGGACTGGAACCAGAGCACCCTTGACTGT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575946.5 5/2
CACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575946_1.fastq

Printing command:
fastqc --outdir SRR6575946_1.fastq

Analysis complete for SRR6575946_1.fastq

Processing SRR6575946_2.fastq

Printing command:
fastqc --outdir SRR6575946_2.fastq

Analysis complete for SRR6575946_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 436M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A6-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 218M Oct 12 19:42 SRR6575946_1.fastq
-rw-r--r--   1 kkarri waxmanlab 218M Oct 12 19:42 SRR6575946_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:03 EDT 2018
0 hours, 0 minutes and 43 seconds elapsed.
==========================================================