-----------------------
Start of variable list:
-----------------------
Sample_ID:
C3-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 19:44:29 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791024
Current job name : Step_02_C3-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/8791024.1.linga

Loading required modules...


List files in scratch directory:

total 87M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  41M Oct 12 19:44 SRR6575779_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  46M Oct 12 19:44 SRR6575779_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575779_1.fastq <==
@SRR6575779.1 1/1
ACTTAGCATCTCAGCTGCCTTGGCCCTCGTGTCCCTGGGAGCAAAGGGCAAGACCATGGAAGAGATTTTAGAAGGCCTCAAGTTCAATCTCACAGAGACC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575779.2 2/1
ATGCGTGTGTGACCCCAGTGCTGACGTTTGAGGAGGCCCTCCACCACCAGCACAACAGAGAACGGGCCTCCTTCATCACTGATGGGGAGCAGCTCCCGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575779.3 3/1
GTACAGCAGGATCCAACCATAGAGAGATAATTCTTGGTGTAAGCAACTAAAAGTGGCAGAGGCGCTTGTCCATAATTGCTGGAATACTCATACAGAAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575779.4 4/1
AGATAACTGTTGCATCCTAGATGAGAGATTCGGTAGTTTCTGCCCAACCACCTGTGGTATCGCAGATTTCCTGTCTTCTTACCAAACCGACGTGGACAAT
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575779.5 5/1
TCTTACTACGGCCTGACTCTGGACGCGTCCGGGCTGGGGCTGACCGTGTACCAGACACAGCTGCTGTTCGGGGCTGTGGAGGTGCCTTCCAAAATTACGG
+
FFF-FFFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFF-FFFFF-FFFF-FFF-FFFFFFFFFF-FFFFFF

==> SRR6575779_2.fastq <==
@SRR6575779.1 1/2
NGTCTGCTGTGAAGGCCTCAGTCTGGTACAGAGCCCTTGTCTTCTCATGGAATTCTGCCAGGATCTGCAGGTCCTTTTCAATAAACATGGCATTGCCTAT
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6575779.2 2/2
CTACGGTGTGCTCCCCTACAGAAGGGTCCCTTTTGGCAGATGGGACGGCAGGAGTTCTGGAAAGCAGAGGTGCAGGGCGGGGGCTCGGGAGCTGCTCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6575779.3 3/2
ATATAGCAGGAAGTTTTCCAGTAGCACATTTGAGCAGGTCAACCAGCTTGTGAAGGAAGTTGTCTCCTTGACTGAGGAGTGCTGTGCTGAGGGAGCTGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575779.4 4/2
GTGGAATTGTGGTCTGCATGCTTATCAAATGAATCTTCTCATTTCCCTGCCAGAACTCTGTGGGGCCAGTTGGCGACAGGGGTCCAAATGCTTATTGATA
+
-FF--FFFFFFF8F8-8FFF8FFFFFF--FF--F-F-FFF-FFF-FF-F-FF--FF-FFF-FF-FFF-FF-FFFF-FFFF-F-F8-F-F-----F--F8F
@SRR6575779.5 5/2
AGTCCTGTCTGTCTGAGCACAGTAGGGTACAACTCAGACGTGAACAGGTAGGCTGTAGTAAAGGCTGCTTCAGAAAAAGCTTTCCCTATCACCACCAGAG
+
F-FFFFFFFFFFFFF-FF-FFF-FFF--FFF--FFFFFFFFFFFFFFFF-FFF-FFFFFFFF-FFF-F-FFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF

Starting FASTQC command


Processing SRR6575779_1.fastq

Printing command:
fastqc --outdir SRR6575779_1.fastq

Analysis complete for SRR6575779_1.fastq

Processing SRR6575779_2.fastq

Printing command:
fastqc --outdir SRR6575779_2.fastq

Analysis complete for SRR6575779_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 461M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C3-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 231M Oct 12 19:44 SRR6575779_1.fastq
-rw-r--r--    1 kkarri waxmanlab 231M Oct 12 19:44 SRR6575779_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:14 EDT 2018
0 hours, 0 minutes and 45 seconds elapsed.
==========================================================