-----------------------
Start of variable list:
-----------------------
Sample_ID:
G6-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 19:46:08 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791205
Current job name : Step_02_G6-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/8791205.1.linga

Loading required modules...


List files in scratch directory:

total 62M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:46 SRR6575263_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  32M Oct 12 19:46 SRR6575263_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575263_1.fastq <==
@SRR6575263.1 1/1
AAGCTGAACAGGGCCAGTCAGACCTACTTCTTCCCCATCCACCTGACGGATCAGCTGCTCCACAGCGCTGAGTTCTACGCCACCGTGGGGCCGCTGGTCG
+
88FFFFFFFFFFFF8FFFFFFFFFFFF88FFFFF8FFFFFFFFFF--F-FF-FFF-FFFF--FF-FFFFF-FFFFFFFFFFFFF-FF--FFFFFF-FFF-
@SRR6575263.2 2/1
GTTAACTCCCTTAGCAAGTGCCCTGTGGGTCAGTGCAGGAGCCCTCCCAACCCCGGCCAGCCCGGGAGGGAGGCAGCTCTGCTCTGCTCTGACATCTGTC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6575263.3 3/1
GTACTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTAATATTTAAGCAAAACTTTATTGTGGCATAGAAAGAAAAAAATTGCACAGGTGGGGTGGGGGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8-8888-F8--FFFF---FF--F-F---------F-FF--FFF-----FF-F--FFF-FFFFF-F-
@SRR6575263.4 4/1
GTGCAAGGGTAATCATTTATTGAACAGGAAGAGGAAGAAATTCATGAAAAATTGTCATGGGTATATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575263.5 5/1
CGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCC
+
FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575263_2.fastq <==
@SRR6575263.1 1/2
NCTCCAGTCCATACAGTGACCAATGAGAAGAGAGAGGTGGCATGTGGGACGTCTACTGGGGAGCACACGAGTCGTCTTCAATTCTACCGCTGTTTCCCAC
+
#FF---FF-FF-8FF-FF-F88-8--FF-F-F-F--F-F--F---F-F--FF---F-F-----FFFFFF---FFFFFFF--F-F-FFF----FFF---F-
@SRR6575263.2 2/2
GGTCCATAGAGAGGGGATGAGACACAGGGACAGGGGCTCAGCCATTGCTCTAGTGAAGCAGAGTCCCAGAGGAGGCATCGCAGGGAGCCTGGGAGGAAAC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6575263.3 3/2
GTCCACAGGCTCACCAAACCCCACCCCTCCTGTGCACTTTGATTCTGTATCTGCCACAATAAAGGTTTGCTGACATAGTCAAGAAAAAAAAAAAAAAAAA
+
FFFFFFFFFFFFFFF-8--FFF-FFFF-FF-FF-FF--FFFFFFFF-F-FF-FFFFF-F-F-FFFFFFFFFFFFF-F-F-FF-FFFFFFFFFFFFFFFFF
@SRR6575263.4 4/2
GGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGGAGCATGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575263.5 5/2
GAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFF-FFF

Starting FASTQC command


Processing SRR6575263_1.fastq

Printing command:
fastqc --outdir SRR6575263_1.fastq

Analysis complete for SRR6575263_1.fastq

Processing SRR6575263_2.fastq

Printing command:
fastqc --outdir SRR6575263_2.fastq

Analysis complete for SRR6575263_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 352M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root       84K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 176M Oct 12 19:46 SRR6575263_1.fastq
-rw-r--r--   1 kkarri waxmanlab 176M Oct 12 19:46 SRR6575263_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:49 EDT 2018
0 hours, 0 minutes and 41 seconds elapsed.
==========================================================