-----------------------
Start of variable list:
-----------------------
Sample_ID:
A7-MAA000907-3_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 19:46:10 EDT 2018
Running on node : scc-ya3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791314
Current job name : Step_02_A7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791314.1.y

Loading required modules...


List files in scratch directory:

total 30M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 A7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:46 SRR6575570_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:46 SRR6575570_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575570_1.fastq <==
@SRR6575570.1 1/1
CNATAAAAGTAAAAACCCCTTGAGAATTAAAATGAACGAAAATCTATTTGCCTCATTCATTACCCCAACAATAATAGGATTNCCAATCGTTGTAGCCATC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFF-FFFFFFFFFFFFFF
@SRR6575570.2 2/1
GTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTGTCTCAGGCTCCCTCTCCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6575570.3 3/1
ATCACATACATCCCCTACTGGATATTCTTAGTTGTGTGCTCATAAGTAATTCAAAGATGTAGCTTGCTCTAAGCTGGGATTGGCATGTTATAAACATGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575570.4 4/1
GCTTTACATAGTGCTGTGTGGCTGGCGTGCAAGGGATGATTTCCTGCCAGTGAGGCCCATACCAGAAGGCCATGTCCTGCTCCAGGGCAGCCCTTCGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575570.5 5/1
CTCGAAAGAGTCCTGTATTGTTATTTTTCGTCACTACCTCCCCGGGTCGGGAGTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTT
+
FFFFFFFFFFFFFFF-FFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF--FFF-F-FFF-FFFF-FF

==> SRR6575570_2.fastq <==
@SRR6575570.1 1/2
NGCTANTATTTATTAATACTAGAGTAGCTCCTCCGATTAGGTGTATTAATAAGTGTCCTGCAGTAATGTTAGCTGTAAGCCGGACTGCTAATGCCAGTGG
+
#F---#FF-FFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFF-F-FFFFFFFFFFFFF--FFFFFFFFF--FFFFFFFFFFFFFFFFFFF-FFF
@SRR6575570.2 2/2
NTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATC
+
#FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6575570.3 3/2
NAACCACAGAGCCTTCCCACATTGGGCACTGCCCATTGTCTACCCTGGGAACCAATGTCTGCAGATAGCATGAGGCCCTAGGAGCTGTGTTCCATGGATA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8FF
@SRR6575570.4 4/2
NAGCCTGAATCGAGCAGAACCAGCCTGAACTAGCCCAGTCCGGTGATGGAGCGTCCACAGCCCGACAGCATGCCCCAGGATTTGTCTGAGGCCTTGAAGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6575570.5 5/2
NATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGG
+
#F-FFF-FFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFF-FFFF8FFFF

Starting FASTQC command


Processing SRR6575570_1.fastq

Printing command:
fastqc --outdir SRR6575570_1.fastq

Analysis complete for SRR6575570_1.fastq

Processing SRR6575570_2.fastq

Printing command:
fastqc --outdir SRR6575570_2.fastq

Analysis complete for SRR6575570_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 164M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 A7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  82M Oct 12 19:46 SRR6575570_1.fastq
-rw-r--r--   1 kkarri waxmanlab  82M Oct 12 19:46 SRR6575570_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:22 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================