-----------------------
Start of variable list:
-----------------------
Sample_ID:
I1-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-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790813
Current job name : Step_02_I1-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/8790813.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 39 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 I1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576430_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576430_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576430_1.fastq <==
@SRR6576430.1 1/1
CTTCCAAGGTTCCTGCTACTATTTCTCTGAGACACAGGCCACATGGGATACAGCACAAAGCTACTGTGGAGGCCAGGGTGCCCATCTGGTGATTGTCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576430.2 2/1
GGTTTGCATAGCAAATTAGCAAGCAAATATTTACATGTTGGTTACATCGTGCCACCCGCTCCAGAAAAGAGTATAGTAGGTATGACCAAGGTCAAAGTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576430.3 3/1
CTCCTGGTGTGGGGGAGGTGGCTTTGAGAACCAACAGAAAGAACTGTTACTTCTTAGGAAATAGTGGTAAAAAGCCAGGTAAGCTGGCTGATAGAGATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576430.4 4/1
GTGCTGAGCAGCTGCTGACCTGGCACCTGCTTGTGAGATGGTTCCATGAGGAGCTCAGGCCTGGCATCCTCCTGTGGCATGGCTGGCCAGACTCTGGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576430.5 5/1
CTTTAATATACGCTATTGGAGCTGGAATTACCGTGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATATAAAGTGGACTCATTCCA
+
-FFFFFF-FFFFF-FFFF8FFFFFFFFF8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFF-FFFF-FFFFFFFFF-FFF

==> SRR6576430_2.fastq <==
@SRR6576430.1 1/2
NGCATGCACTGGTCAGGCTGAGTGGCTCTTATTAATGGTGCATTAGGAAAAACAGCCTTGGTAGTGGGCTCAAGGAATAGGAGCCACCCTTCTGATTCAC
+
#FFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFF-F-FFFF-FFFFFF-FFFFFFF
@SRR6576430.2 2/2
NCGTATTAACTGCTCTCGGCAGCTCTGAGCTTTCCAAAAACTGCCTTAAGTCAGGATCCTGAAGCAATGTCGGATGCTTTACTGTTCTCTGAAGATACCT
+
#FF--FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFF-
@SRR6576430.3 3/2
ATTTAAATCACACCTTTTTAAAAATAAATTTTAAAATTTGGATGCCAATGAACTCTTTGCTGAGTGTCTATAGCATCCTACAACTAGGCATACTCATGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF-FFFF-F-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFF-FFFFFF-F-FFFF8
@SRR6576430.4 4/2
GCCATGTCCTCCTCTGGTTGACGGTGTGTCCGAGTCCATGGAGAGAGGCTGTGCTAGGGTACCCAGCCAAAGACTCGCCTTTGAAGCCTCTGGTGCGGGT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFF---F-FFFFFFFF-FFFF-FFFFFF-FF-FFFFFFF-FFFFFFF-
@SRR6576430.5 5/2
GTACTTGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTAGCAAACATTAAGCCAAGCATGACTAAGTACTCACGGCCGGTACAGTGAACCTGCGA
+
FF-F-FFFFFFFFF8FF-FFFF-8-FFFF-FFF-FF-FF-FFF---FFF-FFFFF-F-FFFFFFF-F-----FF-F-FFF-FF-F--FFF-FF-F--8F8

Starting FASTQC command


Processing SRR6576430_1.fastq

Printing command:
fastqc --outdir SRR6576430_1.fastq

Analysis complete for SRR6576430_1.fastq

Processing SRR6576430_2.fastq

Printing command:
fastqc --outdir SRR6576430_2.fastq

Analysis complete for SRR6576430_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 112M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 39 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 I1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:41 SRR6576430_1.fastq
-rw-r--r--   1 kkarri waxmanlab  56M Oct 12 19:41 SRR6576430_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================