-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M5
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/G160
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 13:35:43 EDT 2017
Running on node : scc-bc1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/02_FASTQC
Current job ID : 468983
Current job name : Step_02_G160_M5
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/468983.1.b

Loading required modules...


List files in scratch directory:

total 2.2G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 13:38 .
drwxrwxrwt. 17 root   root    4.0K Aug 30 13:35 ..
-rw-r-----   1 kkarri pulmseq 1.1G Aug 30 13:37 G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq.gz
-rw-r-----   1 kkarri pulmseq 1.1G Aug 30 13:38 G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq.gz
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 13:38 G160_M5_FASTQC

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq <==
@HWI-D00270:267:CB0DPANXX:4:1101:1410:1917 1:N:0:ACAGTG
NGGGCCTTGAATTCCTGATTTTCAGAGACTTTTATCATGAATGGGTGTTG
+
#=ABBGGFGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1297:1933 1:N:0:ACAGTG
NGGGGACGGACGGGGACCCGGCTATCCGGGGCCAACCGAGGCTCCTTCGG
+
#<=ABGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1449:1968 1:N:0:ACAGTG
NCCCGTCGGGGTCCGACAAAACCCGTCCGCGAGCACACGCACGCGGCAAA
+
#=<ABFFGGGGGGGGGGGFBGGGGGDGGGGGGAGDGEGGGGGGGGGGGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1361:1981 1:N:0:ACAGTG
NCGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGT
+
#=<BBEGGGGGGGGGGGGGGGGGGEGGFGGGGGGGGGGGGGGGGGGGGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1598:1922 1:N:0:ACAGTG
NGGGGATCTGAACCCGACTCCCTTTCGATCGGCCGAGGGCAACGGAGGCC
+
#=ABBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

==> G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq <==
@HWI-D00270:267:CB0DPANXX:4:1101:1410:1917 2:N:0:ACAGTG
CAAGTAGGCTTTATCCTACTTGAAGGATGGTTAAATATACAGAAATCCAT
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1297:1933 2:N:0:ACAGTG
GGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGG
+
BBBBB>FGGGGGGGGGGE>FEFBGGGGGGGGGGF@9CEGGGGGGGGGGEG
@HWI-D00270:267:CB0DPANXX:4:1101:1449:1968 2:N:0:ACAGTG
TTTGTGCCGGGGACGGAGGGGAGAGCGGGTAAGAGAGGTGTCGGAGAGCT
+
CCCCCGGGGGGGGGGGDGGG@EEFGGGGG<EGGEEFGGCGGGGFEGDGEG
@HWI-D00270:267:CB0DPANXX:4:1101:1361:1981 2:N:0:ACAGTG
ACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAA
+
CCCCBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
@HWI-D00270:267:CB0DPANXX:4:1101:1598:1922 2:N:0:ACAGTG
GCTGTAACTTCGTTCACCTCGAATATGTGGAAATATGAACCTCGAATCTG
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

Starting FASTQC command


Processing G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq

Printing command:
fastqc --outdir G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq

Analysis complete for G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq

Processing G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq

Printing command:
fastqc --outdir G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq

Analysis complete for G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 7.8G
drwxr-xr-x   3 kkarri pulmseq 4.0K Aug 30 13:43 .
drwxrwxrwt. 11 root   root    4.0K Aug 30 13:46 ..
-rw-r-----   1 kkarri pulmseq 3.9G Aug 30 13:37 G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R1.fastq
-rw-r-----   1 kkarri pulmseq 3.9G Aug 30 13:38 G160-M5-Index5_ACAGTG-_ACB0DPANXX_L004_001.R2.fastq
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 13:47 G160_M5_FASTQC
==========================================================
Finished on : Wed Aug 30 13:47:03 EDT 2017
0 hours, 11 minutes and 20 seconds elapsed.
==========================================================