-----------------------
Start of variable list:
-----------------------
Sample_ID:
K15-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 19:46:10 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791270
Current job name : Step_02_K15-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/8791270.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 92 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 K15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:46 SRR6576503_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:46 SRR6576503_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576503_1.fastq <==
@SRR6576503.1 1/1
GGACTACAGGCTGTACCTTGGCCATAACTATGTCACTGCCATTCGGAATCAGCAGGAAGGCGTGTGCCCGGAGGGCTCGATCGACAACTCGCCAGTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576503.2 2/1
CATTTACACAGATCTTGCTGTACATGTCAAACTTGACGTTGTAGCCGGCAGCAAACTCCTTGATTTCTTGATTACTACCTGGCTCCTGCCTCCCAAACTG
+
FFF-FFFFFFFFFF8FFFFF8FFFFF8FFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFF-FF--FFFFF-FFFFF-FFF-FFFFFFFFFFFFFF--FFF
@SRR6576503.3 3/1
GTAGCCTTGGGCTTGTGCTTCACCAGCTCAGCAAGAGCCGTTTGTTTCTTAATCTGCTTCTCCTTCTCTGGAAGTGTGCAGATATCAGAGTGGAAGGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576503.4 4/1
TTTTAAATCTTCCAAAAGCATATTTTTATCCCAAACCTAAATTATAACAAATAGCATTAGAATTAGAAAATCTTGGAAGAAAGATAAATGCAGACAATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FF--F-F-FFF-FFFFFFFFF-FF-FFFFFFF-F-FFFF--
@SRR6576503.5 5/1
GGTCAGATGGTTGCCCATCTTCTTGATGAGTTTCACCTCCTTATCCAGATAGTGGCTTTCCAGGAAGTCACAGAGATGAGGGTCCGCGCGGGCAGAACCC
+
FFF-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576503_2.fastq <==
@SRR6576503.1 1/2
NGGATGTTCCAACCAGCGGTTCTGTCTACCCCAGTGTGGCAGGACTTCTTGCCTTTCAGGTTGTTCCAGGTGATGCTAGTGTCCGATGCCTTCACCACAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576503.2 2/2
TGTGTGCATCCCGCGATGATTGGCGCTGTGCGCGCTCCATGCACGAATTCTCAGCCAAGGACATCGACGGGCACATGGTCTGCCTGGATAAGTACAGGGG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF
@SRR6576503.3 3/2
AGACTGCCTTGTGTGGAAGACTATCTGTCTGCAATCCTGAACCGTGTGTGTCTGCTGCATGAGAAGACCCCAGTGAGTGAGCATGTTACCAAGTGCTGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576503.4 4/2
GGCTTAGACTGACACCTCCCGAATAGCATGAGATAGATTTGTTGCTAAGTGGGTGTGGTCAATTGTGTTTCCCCGACGCTGGGTGGTACATAGGGCCTCC
+
FFF-FF8FFFFF8FFFF8FFFFFFFFFFF8FFFFFF-F-FFFFFFF-F-F-FFFFF-F-F-FFFFFFFFFF-FF-F-FFFFFF-FFFFFFFF-F8-F--F
@SRR6576503.5 5/2
GTCTGCACCGTCTCTTCGCGGTTAGCTCCTACTCAGGATCAGCCATGACCTCTCAGATTCGTCAGTATTATTCCACCGAGGTGGAAGCTGCCGTGAACCG
+
FFFF8FFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF--FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576503_1.fastq

Printing command:
fastqc --outdir SRR6576503_1.fastq

Analysis complete for SRR6576503_1.fastq

Processing SRR6576503_2.fastq

Printing command:
fastqc --outdir SRR6576503_2.fastq

Analysis complete for SRR6576503_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 139M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 78 root   root       92K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 K15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  70M Oct 12 19:46 SRR6576503_1.fastq
-rw-r--r--   1 kkarri waxmanlab  70M Oct 12 19:46 SRR6576503_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:33 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================