-----------------------
Start of variable list:
-----------------------
Sample_ID:
L15-MAA000377-3_9_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 19:46:10 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791277
Current job name : Step_02_L15-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791277.1.linga

Loading required modules...


List files in scratch directory:

total 71M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 113 root   root      164K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 L15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576603_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  37M Oct 12 19:46 SRR6576603_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576603_1.fastq <==
@SRR6576603.1 1/1
GGCCAGCCTGGTCTATAGAGTGAGTTCCAGGACAGCCAGGGCTACAGAGAAACCCTGTCTCGAAACCCCCACTCACCCCCCCTCGAAACACGACGAAAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF----------F---FF-FF------F-----FF-F-F
@SRR6576603.2 2/1
CTGTAACCTCTGTGGACATTTGTCTGAATTCTTACCTGGGAGTGAATGGAGGGATGGGGCTAGGTCATTGGAGGATGTTTATGGTTTGTGGTATATTTGG
+
-88FFFF8FFFFF8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576603.3 3/1
GTTTTGTGGATCAGGGTCTCTGAGAGAGTCTGCAGTAGATTTAACTTGGAAGATGACAGAAAACAAAATTCAGATCATGGAATAATTCCAAGGGTGTGTG
+
FF8F-8FFFFFFFFF8FFFFFFF8FFFFFFFFFFFFFFFF8FFF--FFFFFFF-FFFFFFFFFFFFFFF--FFF-FF--FFF-FFF-FFFF--F-F-FFF
@SRR6576603.4 4/1
AGTTAGTAAGGCGCTCCACGATGGGACATTGTGCTTTGCGGAAGCGCTTGGCAGCATACCGTCCGGCACTGTGGGGCAGGTACTTGGCATACTTCTCCTT
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576603.5 5/1
GTACATGGGGATTGCATGAGAGAATCACCTGGAAGAATTTGTGAACAATACTAAAGTTCAGGTGTCACCTTTAGAAATTTAACTAAGGTGACTGGAGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576603_2.fastq <==
@SRR6576603.1 1/2
GTATCAACGCAGAGTACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTGGTATTTTTTTTTTTTGGGGTTAAAAAAAATATTTGTTTTGTTTTTAC
+
F-FFFFFFFFFF8FFFF8FFFFFFFFFFFFF8FFFFFFFFFFFF-----F--F--FFF----F-FFFF--F-F-F-FFFFFF-F----F-8--F-FFFF-
@SRR6576603.2 2/2
GGCTATGGGAGGTGCTATGGGCATAAACAATAGAGGCGCGATGCCCCCTGCTCCTGTGCCACCTGGTACTCCAGCTCCTCCAGGACATGCCACTATGATG
+
FF8FFFFFFFF8FFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFF-FFFFFFFF-F--FFFFFFFF--FFFF-8FF--FFFF-FF8
@SRR6576603.3 3/2
TGGTGGGCACCATCGTCATCATTCAAGGCCTGCGATCAGGTGGCACCTCCAGACACCCAGGGCCTTTATGAGTCACACCCTGGAAAGGAAGGCGTGTGTC
+
FFF-FF8FFFFFF88FFFFFFFFFF8FFFF8FFFFF-FFF-F-FFFFFFF-FFFFFFFFFFFFFFF-FF--FFFFF-F-FFFFFF-8-FFFFFFFF-FFF
@SRR6576603.4 4/2
CGCGTGGTCCACGCCGAGCGACTGAGAAGCCCAGTCTGCGCCCTCAGGATGACTGAGTGGGAAGCAGCCACACCAGCGGTGGCAGAGACCCCTGACATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576603.5 5/2
CCATAGGTTTTTGTTTTGTTTTGTTTTGTAAGTTTTCCTTTTATTTTGCATATGGGAATGTTTTACCTTCATTAAGTAAACCACAAACAAGCAATGCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF-FFFFF-FFF

Starting FASTQC command


Processing SRR6576603_1.fastq

Printing command:
fastqc --outdir SRR6576603_1.fastq

Analysis complete for SRR6576603_1.fastq

Processing SRR6576603_2.fastq

Printing command:
fastqc --outdir SRR6576603_2.fastq

Analysis complete for SRR6576603_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 374M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root      164K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 L15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 187M Oct 12 19:46 SRR6576603_1.fastq
-rw-r--r--   1 kkarri waxmanlab 187M Oct 12 19:46 SRR6576603_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:46 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================