Trouble Shooting

  • When I loaded the massive data, GenomeJack gave an OutofMemory error and quit.

    Please increase the memory size of GenomeJack. You have to edit the start script. Open the start script of GenomeJack and change the value of “-Xmx512m”. If your PC is 32-bit, you set the value up to 1024m. If you load more data, please use a 64-bit PC. If you use GenomeJack in 64-bit PC, please use the “-d64” option.
  • I feel that the position of alignment changes when I zoom in or out the area that GenomeJack displays.

    GenomeJack re-aligns all alignments in the browser and the order of alignments re-aligned is changed whenever you change the area which GenomeJack displays (The order of alignments is the same when GenomeJack displays the same region). This is a feature so that GenomeJack can display the data efficiently.
  • When I change the value of “Feature Limit” in the display property, I feel that GenomeJack becomes slow.

    Please set the value of Feature Limit lower than 200,000. Refer to Change display preferences of each track.
  • I want to import the BED and GTF files which do not meet the constraint condition.

    Please change the extension of your file to “tsv” and import it. However, when you import a BED file as a TSV file, because the BED file has a header, please remove the header rows before you import it.
  • I want to add header information in SAM file.

    Please install SAMtools( in Linux or Mac and execute following commands. “input.sam” is the SAM file before conversion. “reference.fasta” is the FASTA file for reference sequence.

    $ samtools faidx reference.fasta
    $ samtools view -bt reference.fasta.fai input.sam > output.bam
  • I cannot operate GenomeJack through the outside application.

    The following causes are thought to contribute to the cases that you cannot operate GenomeJack through the outside application. Please check the following;
    • Please confirm the URL for connection to GenomeJack. The URL setting in the outside application might be wrong.
    • Please configure the setting of your firewall or change the access port and setting of your firewall. The firewall might close the port for connection to GenomeJack.
    • Please configure and change the setting of your anti-virus software and the access port for connection to GenomeJack. The anti-virus software might close the port for connection to GenomeJack.
  • GenomeJack gave the license error suddenly.

    GenomeJack uses the MAC address etc affiliated with your machine as the license key. When you deleted the network card, GenomeJack could not validate your license key. Please issue a license key again.
    Also it is aware that GenomeJack cannot get the MAC address due to invalidating network adapter. Please validate network adapter if you invalidate wireless network.
  • I want to import the genome data downloaded from UCSC.

    You can import the genome data compressed in the tar.gz format. If you want to import the part of the downloaded genome data, please extract the downloaded data with tar command (such as LhaZ ( for Windows). Please delete the data you do not need in the extracted directory and register this directory when you register the genome data.
  • When Imported the mapping data, GenomeJack gave an error saying [There is no data in the loaded file].

    GenomeJack recognizes the strings from head to space as the name of reference sequence. If the mapping data contains the strings including spaces as the name of the reference sequence, GenomeJack decides that there is no data for registration because the name of the reference sequence is not the same as those in the mapping data. Please check whether there are no spaces in the name of the reference sequence in the mapping data.
  • When I try to show the mapping data, GenomeJack says [Too wide range for drawing features].

    GenomeJack displays only a little mapping data by default so that GenomeJack does not use large memory of your PC. Please change the amount of memory used. Refer to Change display preferences of each track.
  • GenomeJack does not display a root folder for the genome data.

    If you make the genome data unselected, GenomeJack does not display a root folder for it. Please click [File] > [Select Genome...]. GenomeJack displays Select Genome dialog, so please select the genome data to displays in a pull-down list of genome data.
  • I cannot create a new folder in the resource area.

    Please confirm whether the genome data is selected. The genome data may not be selected.
  • When I run the GenomeJACK.jnlp, the message “Error: Could not create the Java Virtual Machin” is displayed.

    There are some causes for being displayed the Error message. They are listed below.
    • It is possible that java 1.6 is installed. Please update to java 1.7.
    • A size described in max-heap-size is bigger than the available memory. Please fix the size described in max-heap-size.
  • When I run the Web Start in 64-bit environment, Java Virtual Machin is created in 32-bit.

    If you install both 32-bit and 64-bit Java, it is possible that 32-bit Java takes priority for some versions. Please update 64-bit Java to the latest version.



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