-----------------------
Start of variable list:
-----------------------
Sample_ID:
O8-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-ka5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790891
Current job name : Step_02_O8-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/8790891.1.linga

Loading required modules...


List files in scratch directory:

total 28M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 102 root   root      128K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 O8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  14M Oct 12 19:42 SRR6576703_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  14M Oct 12 19:42 SRR6576703_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576703_1.fastq <==
@SRR6576703.1 1/1
GGGCTATTGATATTTAACAAATATCCAGCAAAGGTTTTTCCAGGAGATGTAGGAACTCTACCAATTTGAGCATTCTTAGCTGTCTTAGCAGTAGATTATA
+
F--FF-FFFF-FF-FFF8FFFFFFF8F8F8FF88FFF8FF-F8-F---FF--FFF--FFF-FFF----FFF-FFFF-FFF-FFF-FFF-FFFF---FFFF
@SRR6576703.2 2/1
CTCCTTCTCAAACCATAGAACACCTTCTAAATAATGCATGGGATCAAGTTCAGAAAAAGTAGCATGTTCCAACATCTATGTACCAAATTAAAATCAAAAG
+
F8FFFFFFFFFFFF8F-FFF8FFFFFFFFFFFFFFFFF8FFF8FFFFFFFF--FFFFFFFFFFFFFFFFFF-FFFFFFFF-F--FFF-FF-FFF-F-FF-
@SRR6576703.3 3/1
CACCTGGGTTCTCCTCTAAATGGGCCACTTCCACCACAAACCCATGGTTGGTGTGTCCCTGTGTGGTCCACCGCATCACAGCTGGGGTGACGTCGAAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFF
@SRR6576703.4 4/1
GTTCAGCTGTCTCTGTGATCCTGTGATTCTGGGATCCTGTGATCCTGAGATCCTGGGTGTGTCAGAGTTCCTGGGAGTCAAGCTGCCTCTGGGACCCTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576703.5 5/1
GGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF

==> SRR6576703_2.fastq <==
@SRR6576703.1 1/2
CTCTCTCATTGGTTAATACTTCAATAAAAGCCTTGGAAGGGATAGATAGCCACCTATAAAGTATAGCTTCCCATCTACTAAGAGAGTTGTTGGTTTATGC
+
FFF-FFFFF8FFF88-8FFFF8-FFF-FF--FF-FF-----FFFFFFF-F-FF-FFFF-F-FFFFFFFFFFF---F--F--FFFFFF---F-F-FF8FFF
@SRR6576703.2 2/2
CTATTATAGAAGACGAAAATCTACCCCCTCATACTTTTCCTGTTTCTGTACTGTTTAATTGACACTTGTTCTTCCTATGGGGTTCACCAAATACAGTTCC
+
FFFFFFFFFFFFF8FFFFFFFFFF-FFFFF-FF-FFF---F-FF-FFFFFF-FF-FFFFFF-FF-FFFFFFFFFFFFF-FF--F-FF-FFFF-FF-FFF-
@SRR6576703.3 3/2
GCCTCATTCCAGAGCTGGGCCGCAAGAAGTTCGTCGCGGCATCCAGCCGACCCTTGTCCCGGCCTTCGGAAGACGTCCTCAGCGAATTTGAGTTGAGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576703.4 4/2
TGGCATGGCTTCCTTCTGGTCTGGGCTGGTGTCCTGAGCAGACCTTGGGTGCGAACTCCACATCCAGTCCCATAATACCCAGAGGACGCTCCACTCCCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576703.5 5/2
TTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGT
+
FFFFFFFFFFFFFF8-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F

Starting FASTQC command


Processing SRR6576703_1.fastq

Printing command:
fastqc --outdir SRR6576703_1.fastq

Analysis complete for SRR6576703_1.fastq

Processing SRR6576703_2.fastq

Printing command:
fastqc --outdir SRR6576703_2.fastq

Analysis complete for SRR6576703_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 144M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 101 root   root      128K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 O8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  72M Oct 12 19:42 SRR6576703_1.fastq
-rw-r--r--    1 kkarri waxmanlab  72M Oct 12 19:42 SRR6576703_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:41 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================