-----------------------
Start of variable list:
-----------------------
Sample_ID:
D2-MAA100040-3_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 19:44:30 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791069
Current job name : Step_02_D2-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791069.1.linga

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:44 SRR6575174_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:44 SRR6575174_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575174_1.fastq <==
@SRR6575174.1 1/1
CTCTAAGAGTGACTAATTGGTTATCCTGCAGCTATGGTCTATGGTTACACCGCACTTTTATACATAGGTATATAATGTAGTCAAATGTAAATGTTGCCCA
+
F8FFFFFFFFFF--FFF8FF8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F-FFFFFFFFFFFFFFFFFF--FFFFFFF-
@SRR6575174.2 2/1
CAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCGCATTAAATCAGTTATGGTTC
+
FFFF-FFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575174.3 3/1
AGGTGTAGGTCGGGGGCACCACACCACGCTCGCTTGGCAGTAACGCGAGCAGGGGGCGTCCCTATACGCGATGGATCGAGGTCATGACTGGACACTGCAT
+
FF-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575174.4 4/1
GGTTTGGTGTGCATGTCCAAACCACTTCCCCAGCTGCCATGTTTTTCTGAAGCCGGTGGCAAAAATCCCCTTTCTGGGGCCAACTCCTCTGCAATCGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFF-FFF-FFFFFFFF-FFFFF--FFFF-FFFFFFFFFF
@SRR6575174.5 5/1
GTACAAATCATCCTATGTGAAATAAATGCTTATTAAAATCAACAAAATACAATTGGGAAAAAAAAATAAACTTATAATCTGCACTGCTCAGCACTGCACA
+
FFFFF8FFFFFF-FF--8FFFF88F8F8F88FF8FF8FFFFF8F-FFF-FFF----F-F-FF---FFF--F--F--F--F--------FF-F-----FFF

==> SRR6575174_2.fastq <==
@SRR6575174.1 1/2
NGGATGAATGGCTCCCAGTTTTCCAGTTTGAGGTTCGTAGAACAATGTCAAGTGGCAAAATGAAGTTGGTGGACTCCGCCTTAATGAGAAAGGCTTAGAG
+
#-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575174.2 2/2
CGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575174.3 3/2
GTTAGATATTGAGGCTGCTTCGTGTCGGCACGAAGTGTCTTCCGATGCAGTGTCCAGTCATGACCTCGATCCATCGCGTATAGGGACGCCCCCTGCTCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575174.4 4/2
TCTGCATGGCGTGCCCCCTGGAGAGTGTGCCGTGCGTCTGGTGAAAGCAGGCGCCTCCATTGTCGGCGTGAACTGCCACTTCGACCCCAGCGTCAGCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575174.5 5/2
CATACACACACATGAAGAGATGATAAAGATGGCCCACTCAGAATATTTTTTATTATTTTTATAAGGTCCTAATAAGCAAAACAATACTTGCATCATTTCT
+
F8FF-FFFFF8FF8FF8F-F88FFFFF-F-F--FFFFF-FF----FF-FF--F-FF--FF-FFF--F----FF-FFFFFFF--FFF-FF--8F-FF-F-F

Starting FASTQC command


Processing SRR6575174_1.fastq

Printing command:
fastqc --outdir SRR6575174_1.fastq

Analysis complete for SRR6575174_1.fastq

Processing SRR6575174_2.fastq

Printing command:
fastqc --outdir SRR6575174_2.fastq

Analysis complete for SRR6575174_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 155M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:44 SRR6575174_1.fastq
-rw-r--r--   1 kkarri waxmanlab  78M Oct 12 19:44 SRR6575174_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:56 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================