-----------------------
Start of variable list:
-----------------------
Sample_ID:
C6-MAA100039-3_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 19:44:29 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791032
Current job name : Step_02_C6-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791032.1.linga

Loading required modules...


List files in scratch directory:

total 108M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  54M Oct 12 19:44 SRR6576850_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  55M Oct 12 19:44 SRR6576850_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576850_1.fastq <==
@SRR6576850.1 1/1
ATTCTCCTCTGTGATTCCAGAGAGGTCAGCCCCATTGTTGAAGATCCGGGTGATGCCCAGTGGACTCATGAGTGTCTTCAAGTTATAGTCTCCAGAGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576850.2 2/1
TTCTTAGGGTGGTCATTTATGTGTGGGATCTACCACTTTTCCCACAAAGAGGGGGCTCTGAGAGTGTTCTTCAAATATTATGAAAAGGAAAGGGCGGTTG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF
@SRR6576850.3 3/1
GAAGGCCATCTCTGTGGTGCTTGATTTTGTTACCAGTGGCAATTTTCCAGAGTGGTTCAGTTCAAGATCCAAGCTAGTGCACGGGCCCTGATCAGGACTG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576850.4 4/1
TCTCCATTGTGATCCCCTTTCTCTATGTCGGGACACTCATCAGCAAGAACTTCGCTGCTCTGCTTGAGGAACATGACATTTTTGTCCCAGAGGATGACGA
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF---FFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576850.5 5/1
TCAAGAATCAAAGACTTCTTTAAATTTCTCTTTGATATACCCATGACAATTTTTCATGAATTTCTTCCTCTTCCTGTTCAATAAATGATTACCCTTGCAC
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-F--FFFF--FFFF

==> SRR6576850_2.fastq <==
@SRR6576850.1 1/2
TCCAACACCTCCTCCAAACCCTCAACAGACCAGACAGTGAGCTGCAGCTGAGCACAGGCAATGGCCTCTTTGTCAACAATGACCTGAAGCTGGTGGAGAA
+
FFFF-FFFFFFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF8FFFFFFFFFFF-FFFFF8FF
@SRR6576850.2 2/2
TCCCCAGACTGTCCATCTCTGGAAACTATAACTTGGAGACACTCATGAGTCCACTGGGCATCACCCGGATCTTCAACAGTGGGGCTGACCTCTCCGGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8
@SRR6576850.3 3/2
CACCTACTTCATGCCAGCTGCTGAACCACTTCAATTGCCAGCTATCAAGTTGCCAACTGGCAAAGACCTCTGTGGTCAGAGTACCACACAAGCCATGGAC
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF-FFF-FFFFF
@SRR6576850.4 4/2
ACTCTGGGCTCTTGTCACAAACCATGAGGAGGTGAGGCTGAGGGCTTTCCTTGACCCTTCTGCCGACGGGAGGGAGCTGAGCATGCCACCACATCATCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576850.5 5/2
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGGAAGGGTTAAAATTTTTTTTAAAATAAATAGAAAAAAATAAATAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF------------F----F--F-FF--FF-----------FFFFF-FF---FFF

Starting FASTQC command


Processing SRR6576850_1.fastq

Printing command:
fastqc --outdir SRR6576850_1.fastq

Analysis complete for SRR6576850_1.fastq

Processing SRR6576850_2.fastq

Printing command:
fastqc --outdir SRR6576850_2.fastq

Analysis complete for SRR6576850_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 614M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 307M Oct 12 19:44 SRR6576850_1.fastq
-rw-r--r--    1 kkarri waxmanlab 307M Oct 12 19:44 SRR6576850_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:24 EDT 2018
0 hours, 0 minutes and 55 seconds elapsed.
==========================================================