-----------------------
Start of variable list:
-----------------------
Sample_ID:
E3-MAA100042-3_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 19:41:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790768
Current job name : Step_02_E3-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790768.1.linga

Loading required modules...


List files in scratch directory:

total 256M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E3-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 125M Oct 12 19:41 SRR6575624_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 132M Oct 12 19:41 SRR6575624_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575624_1.fastq <==
@SRR6575624.1 1/1
GNATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGTGACTTTTCACCAGGACTCCAGCATCATCCCTTCCTATCCATACAGACTCCCATGCCAAGGTCT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575624.2 2/1
ATCCTAGGTAACATGCTGGAGAGAACGGGATTGCACTTCTCTGTGAGACAGGTGGAGAGCAGATCACAGACCTTGGCATGGGAGTCTGTATGGATAGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575624.3 3/1
GNGCAAGTGTAATCATTTATTGAACAGGACAGGAAAGAAATCAATGGAGAATTTCCATGTGTTGGCAAAGAGAAATTTAAAGAAAGTCTTTGATTCTTGA
+
F#FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-
@SRR6575624.4 4/1
GTCTTGCGCCGGTCCAAGAATTACACCTCTAGCGGCGCAATACGAATGCCCCCGGCCGTCCCTCAAAATCATGGCCTCAGTTCCGAAAACCAACAAAATA
+
FF8FF--FF-FFF-FFFFFFFF8FF8F8F888FFFFFFFFFFF--F-F---F-FFFFFFFF-F---FFF-FF----FF-FFFFF-FFF-F-FF-F-FFFF
@SRR6575624.5 5/1
GGAGTCTGTAGGAGACCTTCGCTGCTGGAGCCATGCCTTCTGTCGCTTTGAAATCTCCGCGCCTGCGCCGGGTGTTCGTGGTCGGCGTTGGCATGACCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575624_2.fastq <==
@SRR6575624.1 1/2
NTATTNAAGTGCAAGTGTAATCATTTATTGAACAGGACAGGAAAGAAATCAATGGAGAATTTCCATGTGTAGGCAAAGAGAAATTTAAAGAAAGTCTTTG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575624.2 2/2
NTATTATATGAACTATGATGGATTCAATACATTTAGTATACTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGGAAA
+
#FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF8F
@SRR6575624.3 3/2
NAATGAGAGCAAGGAGGAGTGTTGAGTGGAGACTTTTCACCAGGACTCCAGCATCATCCCTTCCTATCCATACAGACTCCCATGCCAAGGTCTGTGATCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6575624.4 4/2
NATCTTGGGAGCGGGCGGGCGGTCCACCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGATTCTCTTAGCTGAGTGTCCC
+
#-F-FFFFFFF-F88FF--FF8FFFFFFFFFFFF-FFF-FFF--FFFFF-FF-FF-FFFFFFF--FF--FFFFF-FFF-F--FFFFFFFFFFF-8-F-8F
@SRR6575624.5 5/2
NCTCAAACCCAAGAGCCAACACACAATTTGCCAAGCCTCCTTGAATCAGTTGATGGGCCATAAACAAAGCAGTCGAACCAGTAGAACAGTTATTGTTGAC
+
#FFFFF-FFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575624_1.fastq

Printing command:
fastqc --outdir SRR6575624_1.fastq

Analysis complete for SRR6575624_1.fastq

Processing SRR6575624_2.fastq

Printing command:
fastqc --outdir SRR6575624_2.fastq

Analysis complete for SRR6575624_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.4G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 86 root   root       84K Oct 12 19:43 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 E3-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 715M Oct 12 19:41 SRR6575624_1.fastq
-rw-r--r--   1 kkarri waxmanlab 715M Oct 12 19:41 SRR6575624_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:38 EDT 2018
0 hours, 2 minutes and 10 seconds elapsed.
==========================================================