-----------------------
Start of variable list:
-----------------------
Sample_ID:
F3-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 19:46:08 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791158
Current job name : Step_02_F3-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/8791158.1.linga

Loading required modules...


List files in scratch directory:

total 66M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6576073_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576073_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576073_1.fastq <==
@SRR6576073.1 1/1
GGGTGCAGACGCTGTCTGACCAGGTCCAGGAAGAGCTGCAGAGCTCCCAAGTCACACAAGAACTGACGGCACTGATGGAGGACACTATGACGGAAGTAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.2 2/1
CCTTTAACAGCACACAGTGGGTCCCTTCAGAGCTTGGCATAGTCTTTAAGAATCATCTGTAGTTTCTGGCTCAGCATGATGTTCCCTCTGGCCTTCAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.3 3/1
CAGATAGTGAGGCCATCACAGGAGCAGATCTGCTTGGGGTTCTGGAAAAGGCCGGCAGAGCGTGCAATGATGCCACAGGCCAACCTCTTCCCAGAATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.4 4/1
ATCTAGGAGGCTGCTGACCTCCAACAGGAATTTCACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAGTACTTCTAGCATCAGGTGTTTCAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.5 5/1
CGGATAGGTCTCAGAAAAACGAAATATAGGCTTACGGTAGGTCCGAATGGCACAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCCTAGATGTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576073_2.fastq <==
@SRR6576073.1 1/2
NGTTGGCAGTGCGCTGGCGACCTTGCTCCACCAGAGGCCCCAGGCGCTCACGGATGGCACTCACACCGCGCTCGGCGCCCTCGCGTGCCCCTGCCTTGTA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFF
@SRR6576073.2 2/2
NTTCAAATGCGTACGTGGATCTCGTGCCTGCATCTGGAGTTTCAACCCAGACACCTTCAGAGGGTGGAGAGCTCCAGAGTGCTCTTGTGTTTGGGGAGAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFF-FFF
@SRR6576073.3 3/2
NGTCCGGGCTGAAGCTGGTGGCCGAGCTACCTTCCGGATAGAGGATAAACAGCTGAAGGTGTGGGATGTGATTGGCCGCAGCCTGGTTATCGATGAGGGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.4 4/2
ACCATAGATACCATCTGAAATGGAGAATGATGTTTCAAAGTATTCTGAAGCTTGGAGGATGGTGAAGTAAAGTCCTAGTATAATGGTAATTAGTAGGGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576073.5 5/2
CGTCTCCACACTAGAAGTCGACGAACAACGAAGAGCGACGATGCCCGTTTCAGGTGGTCCTCAGCGTACGGCGGGACCTCTGAGAATTGGGATACAGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF88FFF

Starting FASTQC command


Processing SRR6576073_1.fastq

Printing command:
fastqc --outdir SRR6576073_1.fastq

Analysis complete for SRR6576073_1.fastq

Processing SRR6576073_2.fastq

Printing command:
fastqc --outdir SRR6576073_2.fastq

Analysis complete for SRR6576073_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 392M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 87 root   root      268K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F3-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 196M Oct 12 19:46 SRR6576073_1.fastq
-rw-r--r--   1 kkarri waxmanlab 196M Oct 12 19:46 SRR6576073_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:44 EDT 2018
0 hours, 0 minutes and 36 seconds elapsed.
==========================================================