-----------------------
Start of variable list:
-----------------------
Sample_ID:
I14-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-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791259
Current job name : Step_02_I14-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/8791259.1.linga

Loading required modules...


List files in scratch directory:

total 55M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 I14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:46 SRR6576336_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:46 SRR6576336_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576336_1.fastq <==
@SRR6576336.1 1/1
GNTACAGTTCTGGTCCCTGACGGGGGGGCCTCCTAGCCCTCTGCAGCCTGCTACAGTTCTGAGCGTCTCTCAATCTTGAGCAGCTCCACCTCAAACACCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-
@SRR6576336.2 2/1
GACGTGTTCTTAATTTGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAATGTCCGTGCAAAGTGGTATCCTGAAGTGCGACACCACTGTCCCAATACTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576336.3 3/1
GTACTCGGAGGATGGTGGGCCTTGCTCTGTCTTCTTTGTGGCAACAGACGTGGCAGAGGCGACTGAGGTGTGGACTCCTCGGCGCAGAGCAGCAATGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576336.4 4/1
GATAGTATCTCAACGATTATAGAGAGCCTTTTCTGTCCAAGCTGTCTCATTCCAGTCCTCTAACACCCCTTGAGACCAATTCTGCCACTGTATTTAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576336.5 5/1
CTCCAGATGCTGCATCTTCCCATCATCGGGCAGGAGGAAGACAGCAGTGGCGTTGCCCGCGTAATCCATCAGCAGCACCCAGCTGGAGAGCGTGCTGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576336_2.fastq <==
@SRR6576336.1 1/2
NCACTACACGGGAAAGCTAGAAGATGGGACGGAGTTTGACAGCAGCCTACCACAGAACCAGCCCTTTGTTTTCTCCCTTGGCACTGGCCAGGTTATCAAG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-8FFFFFF
@SRR6576336.2 2/2
NTATTTGACAGCACCGATCTCTTTCGCCATGGCCAGCCCCTGCGGGTAGGTGATGGGAGTCAGCTTCTTCTCCTTCAGCTTCTCAATGGTGTCCTTATCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576336.3 3/2
AGCGGACGCTGTCAGGTCTGTCTGCACTCCCACTCCTGAAGGACCCACACGATGCTTTCTAAACTAGCAAGTCTGCAGACCATTGCTGCTCTGCGCCGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576336.4 4/2
ATATATAACGAAGTGGGTAACACCTTTTGTGAGTAGCCCGTCCAGTTGGATTTTTGTCTGAGATCTTCCACTGGGTTTTTGTTTTTGGTTTTGGTTTTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF
@SRR6576336.5 5/2
GAAAGATAGTTGAGGCTGTGAAAAAACTAGAACAAGACACAGTTTTCGTCCTGGCAAATTACATTCTCTTTAAAGGCAAATGGAAGAAGCCATTCGATCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFF8

Starting FASTQC command


Processing SRR6576336_1.fastq

Printing command:
fastqc --outdir SRR6576336_1.fastq

Analysis complete for SRR6576336_1.fastq

Processing SRR6576336_2.fastq

Printing command:
fastqc --outdir SRR6576336_2.fastq

Analysis complete for SRR6576336_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 299M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 I14-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 150M Oct 12 19:46 SRR6576336_1.fastq
-rw-r--r--   1 kkarri waxmanlab 150M Oct 12 19:46 SRR6576336_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:47 EDT 2018
0 hours, 0 minutes and 37 seconds elapsed.
==========================================================