Query while using NGSQC Tool kit

[SubodhTambat]

Hello everyone,

I am using NGSQC Tool kit for QC of paired end data and I have used following command:

perl IlluQC.pl -pe A4EP_GCCAAT_L004_R1_001.fastq A4EP_GCCAAT_L004_R2_001.fastq N A

During the process it shows

1: Number of reads processed: 0/25111457 (0%)...
TO
1: Number of reads processed: 18000000/25111457 (72%)...

AND

1: Number of reads processed: 24600000/25111457 (98%)...
TO
1: Number of reads processed: 25111457/25111457 (100%)...

So in between 72% to 98% (i.e. from 73% to 97%) it shows a blank space in the command line.

And apart from that following errors occured:

Error:
Can not create image file: ./IlluQC_Filtered_files/A4EP_

GCCAAT_L004_R2_001.fastq_filtered_QualRangePerBase.png
binmode() on closed filehandle I at IlluQC.pl line 1776.
print() on closed filehandle I at IlluQC.pl line 1820.

Error:
Can not create image file: ./IlluQC_Filtered_files/A4EP_GCCAAT_L004_R1_001.fastq_avgQual.png
binmode() on closed filehandle I at IlluQC.pl line 1717.
print() on closed filehandle I at IlluQC.pl line 1766.

Error:
Can not create image file: ./IlluQC_Filtered_files/A4EP_GCCAAT_L004_R2_001.fastq_avgQual.png
binmode() on closed filehandle I at IlluQC.pl line 1717.
print() on closed filehandle I at IlluQC.pl line 1766.
Can not create HTML file: /home/sandor/Desktop/NGSQCToolkit_v2.3.3/QC/IlluQC_Filtered_files/output_A4EP_GCCAAT_L004_R1_001.fastq_A4EP_GCCAAT_L004_R2_001.fastq.html

Please help me with this.

Thank you.

[Brian Bushnell]

I'm not familiar with NGSQC, but perl programs are generally slow. In this case it sounds like you may not have permission to create files in the corresponding directory; make sure your permissions are set correctly.

You can get quality and base-composition (by read position) histograms using bbtools like this:

reformat.sh in1=A4EP_GCCAAT_L004_R1_001.fastq in2=A4EP_GCCAAT_L004_R2_001.fastq out=null qhist=qhist.txt bhist=bhist.txt

Or you can use fastqc which plots neat-o graphs.