-----------------------
Start of variable list:
-----------------------
Sample_ID:
J1-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 19:49:49 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791336
Current job name : Step_02_J1-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/8791336.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 72 root   root      168K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 J1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:49 SRR6576461_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:49 SRR6576461_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576461_1.fastq <==
@SRR6576461.1 1/1
GNGGAGGAAGTCTCTGTTTTGCCCTGTTTCTGCTGAAGTCCTGTGACTTAGAGGGGAAATCGAGGGAATGTGACCTCTCTCNTATCTACTCCTACAGTGA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6576461.2 2/1
GGTTACCAGTGTTCTTTGGGTCATATTCTCATCGACCTTGCATATGACGATGGCGGGGCTGTTCTGTCCAAGTATCTGAGAAATGCTTGTGTACATGACA
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576461.3 3/1
CCTATAATCATCCCGAGAGTAGTCATCCCTGGAGCTCCACGACCGATCATCCCGTCTGTCATAGCGGTCTTCATAGCGGTCCCCACCTCCTCTGTAGTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFF
@SRR6576461.4 4/1
CCACACACCTGCGCAAGATGCGCAAGCGCTTGATGCGGGATGCCGAGGATCTGCAGAAGCGCCTAGCTGTGTACAAGGCAGGGGCACGCGAGGGCGCCGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576461.5 5/1
ATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576461_2.fastq <==
@SRR6576461.1 1/2
NATCANTGCAGCCATACAATGTGCAAAGAGGGTGGTGAGAGATCCCCAAGGCATTCGAGCATGGGTGGCATGGCGAGCACACTGTCAAAACCGAGATCTG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576461.2 2/2
ATTCCGGAACATCAGGGCTACACTCCAAGAACCTCCCTCTGAAGTTTCCATCAGACCCGGGCAGTAAGTCCACTGAAACGCCCACGGAGCAGCTCCTTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFF
@SRR6576461.3 3/2
AACAGACACAGACTGGAGGGCCCGTCCCACCACAGACAGTTTTGATGACTACCCACCTAGAAGAGGCGATGATAGCTTTGGAGACAAGTATCGAGATCGT
+
FFFFFFF-F8FFF8FFFFFF8FFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFF-FFF-FFFFFF-FF-F-FFFFFF-FFFFF-FFFF-FFF8F-FF
@SRR6576461.4 4/2
GGTTGCCCACTTCCTCCAGCCGCCCTCGGATGCGGTCACCAAAAGCCTGGGCGCGATCGCGCAGAGGCTGGGCGGCCCCAGCGCCTAGGTTGGCAGTGCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576461.5 5/2
GCAAAGGCCTCTCAAATTATAAAGATCATGATGAGAACAGCTGTTAGTGAAATAAATGATCCTATAGAAGAGACAGTGTTTCATGTGGTGTAAGCATCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6576461_1.fastq

Printing command:
fastqc --outdir SRR6576461_1.fastq

Analysis complete for SRR6576461_1.fastq

Processing SRR6576461_2.fastq

Printing command:
fastqc --outdir SRR6576461_2.fastq

Analysis complete for SRR6576461_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 124M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 72 root   root      168K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 J1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:49 SRR6576461_1.fastq
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:49 SRR6576461_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:09 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================