-----------------------
Start of variable list:
-----------------------
Sample_ID:
O12-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 19:46:09 EDT 2018
Running on node : scc-wg2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791294
Current job name : Step_02_O12-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/8791294.1.w

Loading required modules...


List files in scratch directory:

total 4.2M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 25 root   root       80K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 2.0M Oct 12 19:46 SRR6576980_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 2.1M Oct 12 19:46 SRR6576980_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576980_1.fastq <==
@SRR6576980.1 1/1
GGGTGAGGTTTCCCGTGTTGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576980.2 2/1
ATCAGGCAGTTTTTGATCACGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGTTTTTTCATGTCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576980.3 3/1
GTACATGGGAGGCAGAGCTGTTGTGGTCAGCTGTGGAAAGGAAGCCTCGTTGCCACCATGAACTTCTCCGGCAAGTACCAATTGCAGAGCCAGGAGAACT
+
FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576980.4 4/1
CATGCCCATCTGCACAGCTTTGTTGAGGTCACAGTCAGCAAAGATGATAAGGGGTGACTTTCCACCCAGCTCCAGGGAGACCTTCTTCACATTACTCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFF
@SRR6576980.5 5/1
GTACATGGGAATCAAGAAATGCACAGTAACTGATGTAACTTGGGCTGCAGTCTGTAATCCACCTCTTCAGCTATAAGTAGGGGACATGTTAAAAAAAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF

==> SRR6576980_2.fastq <==
@SRR6576980.1 1/2
GTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCAAGATTAA
+
FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF8
@SRR6576980.2 2/2
CTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCATTGGCAACAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATTTTTGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576980.3 3/2
ATTTTATTGTCACCTTCCAGCTTGACGACTGCCTTGACTTTTTCCCCAGTCATGGTCTCCAGTTCGCACTCCTCCCCCAGGGTGAACTCATTGCGGACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576980.4 4/2
ATGTTTACATGGCCACCACCTTCGGGGACTTCATCCAGCTCCTAGTGAGGAAGTTGAGAGGGGAGGACGGCGAGAGCGAGTGTGTCATTAACTACGTGGA
+
-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF
@SRR6576980.5 5/2
CCATCAACAGTTTATTATGTGAAGCAGTTTGAGAAAGCTCAGGTCTGGGCCATGATCTTCTCCAGCAGAGTCTTTTTTTTTTTTTTTTTTTTTAAAATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF8--

Starting FASTQC command


Processing SRR6576980_1.fastq

Printing command:
fastqc --outdir SRR6576980_1.fastq

Analysis complete for SRR6576980_1.fastq

Processing SRR6576980_2.fastq

Printing command:
fastqc --outdir SRR6576980_2.fastq

Analysis complete for SRR6576980_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 22M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 25 root   root       80K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 O12-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6576980_1.fastq
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:46 SRR6576980_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:16 EDT 2018
0 hours, 0 minutes and 7 seconds elapsed.
==========================================================