-----------------------
Start of variable list:
-----------------------
Sample_ID:
E6-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 19:41:27 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790770
Current job name : Step_02_E6-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/8790770.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576275_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576275_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576275_1.fastq <==
@SRR6576275.1 1/1
GGTTACCAGCAGTACACTGGGAATTGAAGTGTAAGGGGGTGTGATTGAGCCTAGCCACTGGAGACCCGGCTGCAGCCAGCCTGAGCGTCTCCTTCACTCA
+
FFFFF-FFFFFFFFFFFF88FFFFFFFFFFF88FFF88F8-FFFF-FF-FFFF-FF-FFFFFFFFF-FFFFFFF-FFFFFFFFFFF-FFFFF--FFFFFF
@SRR6576275.2 2/1
GGCACAAGCTGGACGTGGTCTCCTGTGGCAAATCCACAGTCCGAGTGCAGAAGGCCATCTGCAGTGGGTTCTTCCGGAACGCTGCCAAGAAGGACCCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576275.3 3/1
GCATATAGACTCCTAGGAACAGAATTTTTTAATGGTATTTTATAATTTATCAGTCAAGAAAATAATTCATGACTGGAAAAAAATTGCAACCTAAAAGCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFF-FFFFFFF-FFFFFF--FFFF
@SRR6576275.4 4/1
GCCTAGGCCTCCTCAGCTGTGGCATCGATGCCCGCATAGGTGAAGTTCTCAAACAGCGACATGTTCACGTAGGCCTTCCTGGCTTCCAGCATGCGGCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576275.5 5/1
GATCAAGAATGAGAAGCTGCACCAGCAGGACATGAAGCTAATGAAGATGGAAAAGCTGGTGGACAATAACACAGCCTTGGTTGACAAGCTGAAGCGATTC
+
F-FF-FFFFFFFFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFF-FF--FFFFF-FFFFFFFFFFF-FFFFFFFF-FFFF-FFFFFFFF-FFFFFFFFFF

==> SRR6576275_2.fastq <==
@SRR6576275.1 1/2
NTATGTGAGCACTCCAGTAATGAAGCCTCTAGTGCTCCCACATAGTCCTTCTGATACATCCCTCTGCCAGGCCTTCTACCATTGGAAACACTTCCTCTCC
+
#---F-F-F88F88FFFF-888FFFF-F-FF--FFFF-FFFF-FF-FFFFF-FF-FFF-FFFF---FF--F-F--FF---F-----F-F--FFF8FFFF8
@SRR6576275.2 2/2
GAAAATGCTCAGTTTAAGATCAGTCACCACAGGACTAGCTTGTCATCAGTCACAGGAAGCCATGATACAGGAGAGGCAAGTAGTCAGCTGTCTTTCAGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576275.3 3/2
TTCCTATATAGGCCTGGCTTGCCTATAACTTGCTACGTAGACCAGGTAGGCCCCAGACTCACAGAGATCCATCTCCTCCTGCCTCCCAAGAGCTGGAATT
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576275.4 4/2
CCGTCTCCCTGTGCGTTGGATGGCCATTGAGTCCCTCAACTACAGCGTCTATACCACCAAGAGTGATGTCTGGTCCTTTGGGGTCCTCCTCTGGGAGATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576275.5 5/2
GCTATATACAGCTGTTGACTTTTAATACACAGCAGGGTGCGGGGCTATTACAGTCACGTGACACGCCAGTACACCCATTTCACTCACACACACACCCCCC
+
88FF-FFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF-F-FFFF-FFF-FFFFFFFFFFFFFFFFF--FFFFFFFFFFF8FFFFF-F--FF8-FF-FF-F

Starting FASTQC command


Processing SRR6576275_1.fastq

Printing command:
fastqc --outdir SRR6576275_1.fastq

Analysis complete for SRR6576275_1.fastq

Processing SRR6576275_2.fastq

Printing command:
fastqc --outdir SRR6576275_2.fastq

Analysis complete for SRR6576275_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 102M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:41 SRR6576275_1.fastq
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:41 SRR6576275_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:47 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================