Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • SubodhTambat
    Junior Member
    • Oct 2013
    • 8

    #1

    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.

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:13 AM
0 responses
19 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, Yesterday, 10:48 AM
0 responses
18 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Working...