-----------------------
Start of variable list:
-----------------------
Sample_ID:
B2-MAA100040-3_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 19:42:19 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790970
Current job name : Step_02_B2-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790970.1.linga

Loading required modules...


List files in scratch directory:

total 72M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6577018_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:42 SRR6577018_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577018_1.fastq <==
@SRR6577018.1 1/1
TNAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.2 2/1
TCACTGGGCAGTCAGAGTCTCGCTGGCCTTGTCGATCACACTCTGGACTTGGGTCTTAAGCGTCTCCAGCATGGGCATCAGACTATGGCGCAGGTCCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.3 3/1
CCAGACACACTTCTCCTGGAGGAATGTGGCCTGCTGCGCAAGGGGACGGTGCTCCTAGCTGACAATGTCATTGTCCCGGGAACCCCTGACTTCCTGGCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.4 4/1
ATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTCGGGGAAGGGGAAAAAAGTATTTAACCGGAAAAGGTAAAATTTAATGAAAAATTGTCCA
+
F-8FFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FFF8FF--8F-----FF-F-F-F---F-F-FF-F-F---F-F-FFFFFFF-FFFFFFFFFF-F-FF
@SRR6577018.5 5/1
TAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF

==> SRR6577018_2.fastq <==
@SRR6577018.1 1/2
NCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.2 2/2
NTCTGCGCACACAGCTAGCGCCCCACAGCGAACAGATGCGCGAGAGCCTGGCCCAGCGCCTGGCTGAGCTCAAGAGCAACCCTACCTTGAACGAGTACCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.3 3/2
CTGTGATCTACTGCATCTCTGGCCTCAATGCAGCCTTTGATGCACAGGTGTTTTCCAGGGGTATTGTAGTGGTTTGCATGGTGAGCTCACTACCTTTAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577018.4 4/2
ATCCTGGCCTCTGACAAAAGAGAAAAGATAGACGAACATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGTAGAATTCATTAGGTCTTAAAG
+
F--F-FFFF88-8FFFFF-FFFFFF-F-FFFF-FFFF-FFFF-FF-FFFFFFFFFFF-FF-FFFFFF--FFFFFFFFF-FFFFF8F-F---F-F8F-FF-
@SRR6577018.5 5/2
CCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGG
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6577018_1.fastq

Printing command:
fastqc --outdir SRR6577018_1.fastq

Analysis complete for SRR6577018_1.fastq

Processing SRR6577018_2.fastq

Printing command:
fastqc --outdir SRR6577018_2.fastq

Analysis complete for SRR6577018_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 409M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 B2-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6577018_1.fastq
-rw-r--r--   1 kkarri waxmanlab 205M Oct 12 19:42 SRR6577018_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:00 EDT 2018
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================