-----------------------
Start of variable list:
-----------------------
Sample_ID:
H3-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 19:46:10 EDT 2018
Running on node : scc-tk1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791243
Current job name : Step_02_H3-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/8791243.1.linga

Loading required modules...


List files in scratch directory:

total 104M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 50 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:46 SRR6576126_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:46 SRR6576126_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576126_1.fastq <==
@SRR6576126.1 1/1
CNACAGCTTCCACTCTGGCCCTGTGGCAGAGCAGGAAATCGTAAAGTTTAGCCTGCAGAACCTCTACCAGACCTTCTCNACNGGAGGTGGAGGGGGCGAC
+
8#8FFFFFF--FFFFFFFFFFF8FF8FFFFFFFFFFFF8FFFFF-FFFFFFFFFFFFFF-FFFFFFFFFF-F-FF--F#--#FFFFFFF-FFFFF-F-FF
@SRR6576126.2 2/1
TGGCAGGACTTCTTGCCTTTCAGGTTGTTCCAGGTGATGCTAGTGTCCGATGCCTTCACCACAGCCACGGCATAATACCCTTTAGGAAAGATACCTTGTT
+
-F8-FFFFFFFFFFFFFF88FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF--FFFFFFFFFFFFFFFF--F-FFFFFFFFFFF
@SRR6576126.3 3/1
TNCTTGGACATTGTAGGAAGGTTCTCTGGAGCAAAGTGGTGCACAAAGTAGCCTTCCTCAATCTGAATGGAGCCCCCAGAGTCAGACCGGTTGACATCAT
+
F#FFFFFFF--FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576126.4 4/1
GAGCAAGGGTGACACTCACACGCAGATCCTAGAGGGCCTGCAGTTCAACCTCACACAAACATCGGAGGCTGACATCCACAAGTCCGTCCAACACCTCCTC
+
F-FF--FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF8F8FF8F-FFFFFFFFF--FFFFFFFFFFF-FFFFFF-FF-FF-FFFF--FFFFFFFFFFF-F
@SRR6576126.5 5/1
GGCCTACAGTGGTGGCCTGGACACCTCCTGCATCCTCGTGTGGCTGAAGGAACAAGGCGATGATGTCATCGCCTACCTGGCCAACAGTGGCCAGATGGAA
+
FF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FF-FFF-FF--FFFFFF-F-F-FFFFFFFF--FFFFFFFFF-FFF-FFFFFFFF-FF-F

==> SRR6576126_2.fastq <==
@SRR6576126.1 1/2
NGCAGNCACANTCNATGGCCAGAAAGGTCAGCACGCAGTCAGCCAGAGGCACCTGAGCTGACCCCAGCGGGGGTGTCTTGGTCACATCACACCTCAGGAC
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576126.2 2/2
NCATTCGGAATCAGCAGGAAGGCGTGTGCCCGGAGGGCTCGATCGACAACTCGCCAGTGAAGTGGTGTGCACTGAGTCACCTGGAGAGAACCAAGTGTGA
+
#FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFF-FFFFFFFFFFFFFFF-FF-FFF-FF-FFFFF-FFF-F8FFFF
@SRR6576126.3 3/2
NAGCTACCCAGGAAAGCCTTCATCACCAACTTTTCCATGATCATCGATGGCGTGACCTACCCAGGGGTTGTCAAAGAGAAGGCCGAAGCCCAGAAACAAT
+
#FFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FFFF-FFFFFFFFFFFFFFFFFF-FFFF-FF
@SRR6576126.4 4/2
NTGGTGGACTCGTCCACATGGAACTCAGCTTCCTCAGTGTTCTCAGGATCGAATGGCTGTTTCCATTTGCCTTTAAAGAGAATGTAATTCGCCAGGGCGA
+
#FF-FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFF-FF-F-FFFFF-FFFFF-FFFFF--FFFFFFFFFFFF-FFFFFF--FFF-88FF
@SRR6576126.5 5/2
NAATAGCAGGTGAGCTCAAAGCGGACCTGGTCATTCCCCTTTCCCGTGGCGCCGTGAGACACATACTTGGCCCCTTCACGCTGGGCAATCTCCACCTGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFF8FFF

Starting FASTQC command


Processing SRR6576126_1.fastq

Printing command:
fastqc --outdir SRR6576126_1.fastq

Analysis complete for SRR6576126_1.fastq

Processing SRR6576126_2.fastq

Printing command:
fastqc --outdir SRR6576126_2.fastq

Analysis complete for SRR6576126_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 480M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root       36K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 240M Oct 12 19:46 SRR6576126_1.fastq
-rw-r--r--   1 kkarri waxmanlab 240M Oct 12 19:46 SRR6576126_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:39 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================