-----------------------
Start of variable list:
-----------------------
Sample_ID:
G1-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-kb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791194
Current job name : Step_02_G1-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/8791194.1.linga

Loading required modules...


List files in scratch directory:

total 44M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  24M Oct 12 19:46 SRR6576095_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:46 SRR6576095_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576095_1.fastq <==
@SRR6576095.1 1/1
TCAGTGAACAAATCCTGCTATGATAGCAAACACTGCTCCCATTGATAGAACATAGTGGAAATGGGCTACTACATAGTATGTATCGTGAAGCACGATGTCA
+
F-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FFF-FFFFFFFFFFFFFFFFFFFFFF--F-F-FFFFFFFF-FFFFFFFFFFFFF-
@SRR6576095.2 2/1
AGTTTTGACAGATTTTTATTGTGTGCTCAGGCAGCTCACTGGCCATGCAATCCTCTGAGGTAGACTCACAACATCTGGACAGGATTTCAGTAAAGTCTTC
+
FFFFFFFFFFFFF-FFFF8FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFF
@SRR6576095.3 3/1
ATATAGCCTTGTCTAAATTCTCTTGCTGACTCTCTTGTAGACAATGTCGCCCAAAGTCATGGTATTGGTGATTGTGTCTCCATTGAGTTCAGTCACGGAC
+
-F-FFFFFFFF-FFF--FFF88FFFFFF8FFF8FFFFFFFFF8F-FFFFFFFFF-FFFFFFF---FFFFFF-FF-FFFFFFFF-F-FFFF-FFFFFFFF-
@SRR6576095.4 4/1
CTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCA
+
F-8FFF-FFFFFFFFFFFFF8FFFFFFFFFFFFF8FFFFF-FFFFFFF-FFF-FFFFFF-FFF-FFFFFFFFFFFFFFFFFF-F-F-FFFFFFFFFFFFF
@SRR6576095.5 5/1
ACAATTAAGTCAACAGCACATGCAGATAAAAGAAATAGAAAAGCAGCTCAGAAAGACTGGTATTCAAGAACCCTCAGAAAATTCTCTTTCTTCTAAATCA
+
-8FFFFFF-FFF--FFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFF-FFFFFF--

==> SRR6576095_2.fastq <==
@SRR6576095.1 1/2
TTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACCTTTCGGCT
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-F-FFF-FFFFF--FFFFFFFFFFFFFFFFF-FFFF-FFF-FF-F
@SRR6576095.2 2/2
GCTTGTGAAGGAAGTTGTCTCCTTGACTGAGGAGTGCTGTGCTGAGGGAGCTGACCCCACCTGCTACGACACCAGGACCTCAGAGCTGTCTGTTAAGTCC
+
F-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576095.3 3/2
GTACATGGGAGGCAGAGCTGATGTGGTCAGCTGTGGAAAGGAAGCCTCGTTGCCACCATGAACTTCTCCGGCAAGTACCAATTGCAGAGCCAGGAGAACT
+
--FFF-F-FFFFFFFFFFFF8FF8FFFFF-F-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFF-FFFF-FFF8FF
@SRR6576095.4 4/2
GTACATGGGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGCTGCTGCTGCTG
+
F-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFF8F-FF-FF-FFFFFF8-FFFF
@SRR6576095.5 5/2
CATTAAACCCTTGGGAGTTTCTTGGTTTAATAGTGTACACGCCACTTGTATGTTCGCCTCTGTTATAAACGGCAGAGCAGTCGGCAGGAAGGTCATCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF8F

Starting FASTQC command


Processing SRR6576095_1.fastq

Printing command:
fastqc --outdir SRR6576095_1.fastq

Analysis complete for SRR6576095_1.fastq

Processing SRR6576095_2.fastq

Printing command:
fastqc --outdir SRR6576095_2.fastq

Analysis complete for SRR6576095_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 212M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 38 root   root      112K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G1-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 106M Oct 12 19:46 SRR6576095_1.fastq
-rw-r--r--   1 kkarri waxmanlab 106M Oct 12 19:46 SRR6576095_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:37 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================