-----------------------
Start of variable list:
-----------------------
Sample_ID:
L6-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 19:41:26 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790704
Current job name : Step_02_L6-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/8790704.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 104 root   root      164K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 L6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  18M Oct 12 19:41 SRR6576556_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576556_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576556_1.fastq <==
@SRR6576556.1 1/1
GTCCAATGCTGAACTGAACATCATTGCTCAGCAAAAGGCTCCCAAGCCTATGGAAGTCCACATTGTTTTAAGTGCTGGGCATTGGTAATAAGCTAAATTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576556.2 2/1
TCCCAGCACTGAGAATATAGAGGCAGGAGGATCTTTGTGAGTTTGAGGCCAGCCAGTCTACAGCTAGGTCAGCTAGAGTGACAGACAGTAAGACAAGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576556.3 3/1
GCCTCGGCCTCGGCCTCCGGGGCCTTGCGGGGACTCAGCCCTTCGGCGGCTCTGCCACAGGCGCAGCTTCTACTGCGAGCTGCTCCCGCCGGGGTTCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFF-FFFFFFFF--FFFF
@SRR6576556.4 4/1
GTTCTGGTGCTACAGTTCCTCTCCAACAAGAATATGGCACACTGGCCAGCACAAGCCATGCTAACACTGAGCCTCCAGCACTGGGCACAGATTCGGATCT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576556.5 5/1
TATCAACGCAGAGTACATGGGGTCGAGTCGCGTCCACCCGCTAGCACAGCTTCTTTGCAGCTCCTTCGTTGCCGGTCCACACCCGCCACCAGTTCGCCAT
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576556_2.fastq <==
@SRR6576556.1 1/2
NGGCCATGGCTCTGTAATTCACTTGCTTTGTCTCTCTCTCACTGTCTACATGAACTAGCCACTCAGCATCCCTTAACTCACCATTGTGTTGCTCTTACCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576556.2 2/2
NTTTTTAAGTTATTGGTTAAGTAACAGTAATGATTTATCAAAAAACCTGCATGTTTTTGATATTAATTGATGTGTTTCTGCTAGTTAATCTTGCATAGCC
+
#-F-FFFF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFF----FF-FFF--FF-FF-FFFFFFFFFFFF---FF-FFF-FFFFFFFFFFFFF8F-FFFF--
@SRR6576556.3 3/2
CTTTACTACCAGTTATTACCCCATGTGTACAACTGCAAGAAAAGGTTCCCATGTACACACAGGCAGTGAGAGAAACTTACTGTTTGGTTGTTATAGGAGC
+
FFFFFFFF-8FF888-F-FFFFFFFFFFFFFFFFF---F--F-FFFFFFFFFF--FFFFFF-FFFFFF-FFF-FFFF-FFFFFF--F------FFFF---
@SRR6576556.4 4/2
CAACAGCAGTTTGTAGAGAGAATTTTATGCATATGCTGGTAATTTTTTCCCTGTGTTTACATCTTGAGACAGAAGAGTTTGCAGCTACATGGTGGGCTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576556.5 5/2
TTCCCACCATCACACCCTGGTGCCTAGGGCGGCCCACGATGGAGGGGAATACAGCCCGGGGAGCATCGTCGCCCGCGAAGCCGGCTTTGCACATGCCGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576556_1.fastq

Printing command:
fastqc --outdir SRR6576556_1.fastq

Analysis complete for SRR6576556_1.fastq

Processing SRR6576556_2.fastq

Printing command:
fastqc --outdir SRR6576556_2.fastq

Analysis complete for SRR6576556_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 196M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 L6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576556_1.fastq
-rw-r--r--    1 kkarri waxmanlab  98M Oct 12 19:41 SRR6576556_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================