-----------------------
Start of variable list:
-----------------------
Sample_ID:
G2-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 19:46:10 EDT 2018
Running on node : scc-yh2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791325
Current job name : Step_02_G2-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/8791325.1.y

Loading required modules...


List files in scratch directory:

total 37M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:46 SRR6576354_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:46 SRR6576354_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576354_1.fastq <==
@SRR6576354.1 1/1
GGCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTTGGTGACTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576354.2 2/1
ATAGAAGAGACAGTGTTTCATGTGGTGTAAGCATCTGGGTAGTCTGAGTAGCGTCGTGGTATTCCTGAAAGGCCCAGGAAATGTTGAGGGAAGAATGTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576354.3 3/1
TATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576354.4 4/1
GTCTAAGCTTCTCTGGCATGCCTGTCTGAGCTTCTCTGGCCTGTCTAAGCTTCTCTGGCACATGTTTAAGAGAAGCTTTCTGAAGACTTTTGATGTAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576354.5 5/1
GCTCTGAGGGCTCATGCTCATGTCTGACGACGTCTCATCCATGTCCAGCTCATCGGAGGACTCTCTGCTTTCTGAGGGCCCGCTGAACTTCCGTCGCGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576354_2.fastq <==
@SRR6576354.1 1/2
ACTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-F-FFFFF-FFFFF-FFFFF--FFFFFFFFFFFFFFFFF
@SRR6576354.2 2/2
ACATGGGCACGATACATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FF--FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFF-FFFFFFF8FFFF
@SRR6576354.3 3/2
GTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576354.4 4/2
GATGAATTCTTTGAATCTAAGGTATTGACTATGTCTGTTGTGTCTGGGCTAGACCGACTACAAATAACTTATAATTATGACATATATTTTCTGGCACATT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFF-F-FF8FF
@SRR6576354.5 5/2
CTGGTAACCAATGCAGCCATGCAAGGGATAGGATTAAACATAGCTCAAGTGCTTGGGCAGCACACGGGCTTGGAAAAATACCCTCTTTGGAAAGTACCTC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576354_1.fastq

Printing command:
fastqc --outdir SRR6576354_1.fastq

Analysis complete for SRR6576354_1.fastq

Processing SRR6576354_2.fastq

Printing command:
fastqc --outdir SRR6576354_2.fastq

Analysis complete for SRR6576354_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 195M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 35 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:46 SRR6576354_1.fastq
-rw-r--r--   1 kkarri waxmanlab  98M Oct 12 19:46 SRR6576354_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:24 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================