-----------------------
Start of variable list:
-----------------------
Sample_ID:
H5-MAA100138-3_56_F-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 19:46:09 EDT 2018
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791246
Current job name : Step_02_H5-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791246.1.linga

Loading required modules...


List files in scratch directory:

total 136M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 47 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:46 SRR6575917_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  70M Oct 12 19:46 SRR6575917_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575917_1.fastq <==
@SRR6575917.1 1/1
TNGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACNAAAGTCTTTGGGTTCCGG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575917.2 2/1
TCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAAATTAGAGTGTTCAAAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575917.3 3/1
TAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCACGGAATCGA
+
FFFFFFFFFFFFFFFFFF8F88F8FF8F8FF8F8F-8FFFFFFFFF-FF-FFFFFFFFFFFFFFF-FFFFF-FFF-F---F-F-FFFFFFFFF-F--FFF
@SRR6575917.4 4/1
GCCTGTGTTTAATGGAAGGAACCCAATTCAGAAGGAAGGATGACATCGTAGGGTGGTCATTTATGTGTGGGATCTACCACTTTTCCCACAAAGATGGGGC
+
F8F-FFFFF-FFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFF-FFFFFF-F-FFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6575917.5 5/1
CAGGTGGGCCCCTTGGGATCATGCAGGCTGTCCTGGACCACACCATTCCCTACTTGCATGTGAGGGAGGCCTTTGGCCAGAAGATCGGCCAATTCCAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575917_2.fastq <==
@SRR6575917.1 1/2
NCACGNAATCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575917.2 2/2
NTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F-FF
@SRR6575917.3 3/2
GACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAAC
+
FF-FF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FF-F-FFFFFFF-FF---F--F-F-F-FFFFF88
@SRR6575917.4 4/2
CGGTCAACTTAGCAGAGTCCGAGGAGGCCAAGCACGTGCGCCATGATTGAGGGGAGAAGGGAACCCAAGGAAAGATAGATGAGGCAGTCAAAGCACTGGA
+
F-F-F----88-FFF-8-F8FF-FF--FF-FF-----F---F-FFF-F--F-FFF--FFFFF-FFF-FF-F-F-FFF-F-FFFFF-FF-FFFF-----F8
@SRR6575917.5 5/2
TTCCTGCCCGGAACGGCTGGAGAATCCGACTTCACACGGGGCAGAGGGCTGACAGAGAAGGGCAGCTGAGCAGCAGAGCTTCCTTAGACAGGTCAGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575917_1.fastq

Printing command:
fastqc --outdir SRR6575917_1.fastq

Analysis complete for SRR6575917_1.fastq

Processing SRR6575917_2.fastq

Printing command:
fastqc --outdir SRR6575917_2.fastq

Analysis complete for SRR6575917_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 748M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 44 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H5-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 374M Oct 12 19:46 SRR6575917_1.fastq
-rw-r--r--   1 kkarri waxmanlab 374M Oct 12 19:46 SRR6575917_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:46 EDT 2018
0 hours, 0 minutes and 37 seconds elapsed.
==========================================================