-----------------------
Start of variable list:
-----------------------
Sample_ID:
F7-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 19:46:08 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791175
Current job name : Step_02_F7-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/8791175.1.linga

Loading required modules...


List files in scratch directory:

total 100M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 29 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:46 SRR6576082_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:46 SRR6576082_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576082_1.fastq <==
@SRR6576082.1 1/1
CGCCTTCGGTGACATGACCAATGAGGAATTCAGGCAGGTGGTGAATGGCTACCGCCACCAGAAGCACAAGAAGGGGAGGCTTTTTCAGGAACCGCTGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576082.2 2/1
CCAGTGTCTTCTCTCCCATTTGTAATTTTGTTTTTCTTCCTGCTCTGTTTTTTCTTTTGCCATGGTGGACCTGCATAAGAGCGATCCCTAATAACCACGT
+
FFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFF--FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFF
@SRR6576082.3 3/1
CTTGTAGACTTCTTCTTGTGCAAAAGAAAAAGAGAAAGTAAAAAGAAAAAAAAAAAGTCCCCAAATGCCATTTATTTAGCCACAGAGTACTTTGCTATCA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFF-FFF-FFFFFF
@SRR6576082.4 4/1
GGCCTGCACATCACATAATTTTGTCTTGATTTAGAATAATCAATGGGAATATCCACCTATGGAGGCCTTAATCAGAAAGTATGTGTGTGCAAACATAACA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576082.5 5/1
TATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576082_2.fastq <==
@SRR6576082.1 1/2
NCCGAGTCCAGACCTCCATTTTCCTTAATGTACTGGAAAGCAAAATCCATCAGGCCTCAGTTACAGCCCTGATTGCCTTGAGCGTGAGAACAGTCCACAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576082.2 2/2
NCTAGGCTCTAGACCTTTAATGTGCTATTTTGGTAAACAATGGGGCTGATTTCTGCCCACACCCTAAAAACGTATCTGAGGCTGAATGTATAAAGCTATG
+
#FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFF-FFFF-FFFF8FF
@SRR6576082.3 3/2
NAACAAGAAGGTGACCAAGATGGAAATCCTGCAGCACGTCATCGATTACATCTTGGACCTGCAGATCGCCCTGGACTCGCATCCCACTATCGTCAGCCTG
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576082.4 4/2
GTTAAGGAAAGGCCCAGAGGGACATCAAATCACAGATGTGGTTTCCACTGCTTTTGGTTGCATGTTGGAACTGGAGAACTCCTTGCTGAGGACATGACCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576082.5 5/2
GTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6576082_1.fastq

Printing command:
fastqc --outdir SRR6576082_1.fastq

Analysis complete for SRR6576082_1.fastq

Processing SRR6576082_2.fastq

Printing command:
fastqc --outdir SRR6576082_2.fastq

Analysis complete for SRR6576082_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 548M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 25 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 274M Oct 12 19:46 SRR6576082_1.fastq
-rw-r--r--   1 kkarri waxmanlab 274M Oct 12 19:46 SRR6576082_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:40 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================