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How avoid the warning "WARN 11:38:44,636 Mimetypes - Unable to find 'mime.types' file in classpath"

mandormandor Member
edited July 2012 in Ask the GATK team

Hi,
I have this warning : WARN 11:38:44,636 Mimetypes - Unable to find 'mime.types' file in classpath , to configure properly, what I have to do?
I just run the first walker (works fine, and it is quick in execution), but then, it spend so much time in "GATKRunReport" phase. (could be caused by this warning ?..).
Thanks!,
-- Mandor

Best Answers

  • SophiaSophia Member
    Accepted Answer

    This is most likely about the remote connection to the Broad Servers that store the run reports.
    Try to use -et NO_ET to switch this functionality off and avoid (possibly) the error.

    cheers,
    S

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Proxies are a common problem for the "phone-home" feature, yes. It is possible to get a key to deactivate this feature on request so you don't have to do any hacking.

    FYI, the reports are interesting for us even when there is no crashing. They tell us what tools are most popular, where the biggest performance issues are and so on, and knowing all of this helps us focus on improving the GATK in the ways that are most useful to the user community.

    Be sure to update often! We continuously fix bugs and improve accuracy and performance, so it's in your best interest.

Answers

  • mandormandor Member
    edited July 2012

    Just more detailed case :

    Of course, every time that I run the GATK command it gives this warning and spend so much time at "GATKRunReport step", although the programs usually works as expected :).

    Here a sample of one :

    $ java -cp /home/armand/biotools/GATK_1.0/GenomeAnalysisTK.jar:CustomPackage.jar:. org.broadinstitute.sting.gatk.CommandLineGATK -T PlayReads \
    -I ./test/test_0.bam \
    -R /home/mandor/mnt/cubix/Genomes/hg19/Homo_sapiens_assembly19.fasta

    INFO 15:43:25,785 HelpFormatter - ---------------------------------------------------------------------------
    INFO 15:43:25,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5506, Compiled 2011/03/24 17:21:22
    INFO 15:43:25,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 15:43:25,790 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
    INFO 15:43:25,791 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
    INFO 15:43:25,791 HelpFormatter - Program Args: -T HelloRead -I ./test/test_0.bam -R /home/armand/mnt/cubix/Genomes/index/index/hg19/bwa_path/Homo_sapiens_assembly19.fasta
    ......

    INFO 15:43:26,805 GATKRunReport - Aggregating data for run report
    INFO 15:43:26,934 GATKRunReport - Posting report of type STANDARD
    INFO 15:43:27,179 GATKRunReport - Wrote report to ./UQC36dyuzydnwhPXMQIMZ8EoLyTm2Nmi.report.xml.gz
    INFO 15:43:27,179 GATKRunReport - Generating GATK report to AWS S3 based on local file ./UQC36dyuzydnwhPXMQIMZ8EoLyTm2Nmi.report.xml.gz
    WARN 15:43:27,301 Mimetypes - Unable to find 'mime.types' file in classpath
    alled bases of all loci 0.002
    INFO 15:25:46,521 UnifiedGenotyper - % confidently called bases of all loci 0.002
    INFO 15:25:46,521 UnifiedGenotyper - % confidently called bases of all loci 0.002
    INFO 15:25:46,521 UnifiedGenotyper - % confidently called bases of all loci 0.002
    INFO 15:25:46,521 UnifiedGenotyper - % confidently c
    WARN 15:44:28,669 GATKRunReport - A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is: S3 exception occurred. Error message is: Request Error.

  • SophiaSophia Member
    Accepted Answer

    This is most likely about the remote connection to the Broad Servers that store the run reports.
    Try to use -et NO_ET to switch this functionality off and avoid (possibly) the error.

    cheers,
    S

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Mandor, I notice you are using a very old version of GATK (v1.0.5506). I would strongly recommend you update to the most recent version (2.0.x), otherwise we really can't help you.

  • mandormandor Member

    Thanks to all, Sophia point the good answer. I am using a proxy to go outside the net, so the program stay "on the air" too much seconds. I fixed it using "-et NO_ET" option.
    Also I think that it could be better maybe that by default doesn't make this automatic reports, and only when it crashes, the end user specifically repeat the operation to send you this result (I don't know .. or re-writing this class.).

    But anyway, I will update to latest version :)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Proxies are a common problem for the "phone-home" feature, yes. It is possible to get a key to deactivate this feature on request so you don't have to do any hacking.

    FYI, the reports are interesting for us even when there is no crashing. They tell us what tools are most popular, where the biggest performance issues are and so on, and knowing all of this helps us focus on improving the GATK in the ways that are most useful to the user community.

    Be sure to update often! We continuously fix bugs and improve accuracy and performance, so it's in your best interest.

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