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  • SubodhTambat
    Junior Member
    • Oct 2013
    • 8

    Query while using NGSQC Tool kit

    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.
    Last edited by SubodhTambat; 04-17-2014, 11:24 PM.

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