-----------------------
Start of variable list:
-----------------------
Sample_ID:
B8-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-ya3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790997
Current job name : Step_02_B8-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/8790997.1.y

Loading required modules...


List files in scratch directory:

total 41M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:42 SRR6577031_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:42 SRR6577031_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577031_1.fastq <==
@SRR6577031.1 1/1
CTATAACTGCGGTAGAGGTGGCCACATTGCCAAGGACTGCAAGGAGCCCAAGAGAGAGCGAGAGCAATGCTGCTACAATTGTGGCAAGCCAGGCCATCTG
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577031.2 2/1
AGTGGGGACCATGGCAAGAGACTGTTTGTCGTCAAGCCTTCTTTATACTATGACGCTCGCTTCTTGAGGTTAATGAAATTCTACCTTATGTTGACTGGGA
+
F-F-FFFFFFFFFFFFFFFFFF888FFFFFFFF88FFFFFFF8F-FFFF-FFFFFFFFFFFFF-FFFF-FF-FF-FFFFFFFFF-FFFF--F-FF-F-FF
@SRR6577031.3 3/1
CTCCACCATCATCCCTTCCTATCCATACAGCATCCCCAGTATAAATTCTGTGATCTGCATTCCATCCTGTCTCACTGAGAAGTCCAAATCCAGTCTATCC
+
FF8-FF--FFFFFF8F-F8FFFFFF8FFFFFF8FFFFFF8FFFFF-FFFFF-FFFFFFFFFFFF-F-FFFF-FFFF-FFF-FFFFFF-FFF-FFFFFFFF
@SRR6577031.4 4/1
GGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTGTCAATCCTGTCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFF--FF-FFFFF-FFFF--FFFFFFFFF-F---FFF
@SRR6577031.5 5/1
ATATTAGGATCTGGCTCATAACCCTTTGGAGTAGCTGCTTGAAGGTGCATCCCGAATTTTGCAGCACTCATCATGATAGAGTGCAAGATATTGTTCCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577031_2.fastq <==
@SRR6577031.1 1/2
NCACTGCAAGTAAAGCTCACTGGCCTGGGAACAGCCTCTATCTGCCAACCTTTGGCCAGTGAAGAGGATTCAGAGAAAATAATACAACCATCAATCAGAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFF
@SRR6577031.2 2/2
CACCAGTGTTATGCCAAAAATAACAGGGATCCCAGTCAACATAAGGTAGAATTTCATAAACCACAAGAATCGAGCGTCATAGTATAAAGAAGGCATGACG
+
FF--F-F-FFFF8F8FF--FFFF8--F-F-FFFF-FFFFFFF-FFFFF-FF--FF-F-FFFF-FFFFFF-FFFF---FF-FF-F8FFF-FFFF--8F8F8
@SRR6577031.3 3/2
GAACAGGAAGAGGAAGAAATTCATGAAAAATTTTCATGGGTGTATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATG
+
8F-FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFF-FFFF-FFFFFF-F8FFF-F
@SRR6577031.4 4/2
GTGTCCCGCGGGGCCCGAAGCGTTTACTTTAAAAAAATTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGAGACCGCAGCTAGGAATACTGGAATAGGAC
+
8FFFFFFFF8FFFFFFFFFFF8FF-FFFFFFFFF-FF--FFFFF-F-FFFFFFFFFFFFFFFF-FFF-FFF-FFFF-FF-F--F---F-FFFFF-F8F-F
@SRR6577031.5 5/2
GGCCCCCACTGCCTGCCTGCCTGCCTGTGGAGCTCTCTAGACCACAGATTCCTCCTTCACTCTAGCAAAAAGAAGATGCTGTCTAATTTGAGGATCCTGC
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFF-FF-FFF-FFFFFF-F-FFFFFFFF-FF-FFFFFFFFFF-FFF8--

Starting FASTQC command


Processing SRR6577031_1.fastq

Printing command:
fastqc --outdir SRR6577031_1.fastq

Analysis complete for SRR6577031_1.fastq

Processing SRR6577031_2.fastq

Printing command:
fastqc --outdir SRR6577031_2.fastq

Analysis complete for SRR6577031_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 244M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B8-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 122M Oct 12 19:42 SRR6577031_1.fastq
-rw-r--r--   1 kkarri waxmanlab 122M Oct 12 19:42 SRR6577031_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:33 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================