-----------------------
Start of variable list:
-----------------------
Sample_ID:
O1-MAA000907-3_11_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 19:42:18 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790885
Current job name : Step_02_O1-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790885.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 O1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:42 SRR6576687_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:42 SRR6576687_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576687_1.fastq <==
@SRR6576687.1 1/1
GTGTGTGTGTGTGTGTGTATGTGTGTTTAAGTTGTTTGTTTGTTTGACAGGGTCTCCCTATGTAGCCTTGGCTGGCTTGGAACTTGCTCTGTAGACCCAG
+
-8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576687.2 2/1
ATGTAGCCCAGGCTAGCCTTGAACTCTCCAAGTAGCCTGAGCTGGCCTTATACTTGTGATCCACCTGCTTTTGACTCTAGAGGGCCAGAGACCCTGTTTT
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576687.3 3/1
GGGAAGGACACCTCCCTCATTCTCCCTGTTCCTTTCTTACAACGAAATACCTCGTTTGTGGTGTAACTGGGCCACTAATATAAGGAGCTGGGAATGTCAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576687.4 4/1
TTACTCTATCGCTTCCAGATATGGAGGCCGTTCACTGCAACCTTTTACTTCACCGTGGGCCCAGGGACTTGATTTCTGTATTTGGTAAATTTATATTTCT
+
FF--FFFFFFF-FFFF-FFFFFFFF8FF8FFFFFFFFF88--FF-F-FFFF-FF-FF--FFF-F-FF-F-FFF---F-FF-FFFF----FF-FFFFFFFF
@SRR6576687.5 5/1
GCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGACATCGTGCTTCACGATACATACTATGTAGTAGCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFF

==> SRR6576687_2.fastq <==
@SRR6576687.1 1/2
CTCCACAGACAAGGCCATCAGAACACGCTCTTGCAGCAGACACTGCTGTATGTGACTCTCCACCACTTGAAAGAACAGTGGCTTCTTACAAACCATTTAT
+
FFFFFFFF-FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFF-FFFFFFF-FF
@SRR6576687.2 2/2
ACTGAGAACACATCTCAGTACCAGGGAGTGGTTGTCTATTCCATGGCGGACATTCCTCTGGGTTTTGGGGTGGCAGCAAAGTCTACCCAAGACTGCCGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576687.3 3/2
CCTTTAAATACTCTATACTGGGGTTGAGATTTTAGGTCACAATTATTAGGTATCTAGGAGATCATGAGTTATGCTCTTAGTCATTCATTATTTTAGGGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-88FF
@SRR6576687.4 4/2
GGACAGAAAATTCCTTCCTCACAAGTCCATTTGGTATCTGAACATCAGGATGAAATAAAGATGGCCGACAAGGTTTCCATTGAGCTCATTGATCACCGAG
+
-8FFFFFFFFF-FFFFFFF88FFFFFFFFF--F-F-F-FFF---FF-FFF-F-----F-F-FF--FF---F-F-FFFFF--FF-F-FFFFF8F---F-F-
@SRR6576687.5 5/2
CATGTGGTGTAAGCATCTGGGTAGTCTGAGTAGCGTCGTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAATGTTATGTTTACTCCTACGAATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576687_1.fastq

Printing command:
fastqc --outdir SRR6576687_1.fastq

Analysis complete for SRR6576687_1.fastq

Processing SRR6576687_2.fastq

Printing command:
fastqc --outdir SRR6576687_2.fastq

Analysis complete for SRR6576687_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 130M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 O1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:42 SRR6576687_1.fastq
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:42 SRR6576687_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================