-----------------------
Start of variable list:
-----------------------
Sample_ID:
D15-MAA000377-3_9_M-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 19:44:28 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791061
Current job name : Step_02_D15-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791061.1.linga

Loading required modules...


List files in scratch directory:

total 22M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:44 SRR6575370_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:44 SRR6575370_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575370_1.fastq <==
@SRR6575370.1 1/1
CCCATATTGAAAGGTCTCGCAGGCCATGGAAGCGCCGTTGTAGTAATACCTCTCTTGCATCCCTAGGCAGGGGCCTTCTGAGTAATTGAGCTGGCAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575370.2 2/1
CCAGTGAGATGCGGAGTGAGCTGTTGGGCATGGAACCATCTGGAGAATGTGAGGTGGACATGAGGAAACGAGCTGCGAAGGGGTCCAGACCTGCAGATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575370.3 3/1
CCAGGGACACTCCCAGGATGGCATTTGCACCAAATTTAGATTTATTCTCTGTGCCGTCCATCTCGATCATCAGCTTGTCAATCTTCTCTTGCTCCACAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575370.4 4/1
GTGGGGAGGAGGCGAACAGCAGGCCCGTGGTTCAGCCTCATCCCTCCGGCAGCCTTATCATTGACAAGGACTCTGAAGTTTACAAGATGCTTCAGGAGAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575370.5 5/1
CTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575370_2.fastq <==
@SRR6575370.1 1/2
CCAAAGACCACAGAGCCATGCAGGGTCTCAGGACCCTGTTCCTGCTGCTGACTGCCTGCCTCGCTTCGAGGGCTGACCCTGCGTCAACACTGCCAGATAT
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFF8FF--FF-
@SRR6575370.2 2/2
CTCCAGGTTCTGGTCTGCCATCTTGAGTGAATGTGACAGGGTCTGATTGTCCTTCTTGATGACACTCTGGGCAGCCAGTGTGTTGGTCTTGAGGCTGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575370.3 3/2
TTGCAGCGATCCTACTGCCAGAAATTCGCCATGTCTATTCTCAGGATCCACGCCAGAGAGATCTTTGACTCCCGTGGGAATCCCACTGTTGAGGTCGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFF-FFFFFF8FF-FFFFFFFF-F
@SRR6575370.4 4/2
GCATTCAGGGTGGCGATGGTGATCCCTCAGCTTCACAAACACACCAACAATACCAGTTCCACATTTGTCACAGATGGGCAGCTTCTGAGCATTTCCAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575370.5 5/2
ATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGCCG
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFF

Starting FASTQC command


Processing SRR6575370_1.fastq

Printing command:
fastqc --outdir SRR6575370_1.fastq

Analysis complete for SRR6575370_1.fastq

Processing SRR6575370_2.fastq

Printing command:
fastqc --outdir SRR6575370_2.fastq

Analysis complete for SRR6575370_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 120M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 86 root   root       92K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:44 SRR6575370_1.fastq
-rw-r--r--   1 kkarri waxmanlab  60M Oct 12 19:44 SRR6575370_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:52 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================