Re: [galaxy-dev] Visualisation of VCF files in trackster
Thanks for reporting this issue and workaround Ulf. I've committed a fix that addresses this issue by only includeing the -split option for BED/GFF/GTF datasets and not VCF: https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643de8a08fa41662e71 Best, J. On Sep 12, 2013, at 6:45 AM, Ulf Schaefer wrote: Dear Jeremy Thank you for your reply and sorry for not being clear. In short I solved the problem. Below is some info, in case this is useful for someone else. Thanks for your help The situation was: On Main: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - OK On my local install: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - FAIL The reason is that this command fails: grep -v '^#' /data/database/files/000/dataset_596.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /data/database/files/000/dataset_598.dat temp.bg ; bedGraphToBigWig temp.bg /data/database/files/000/dataset_598.dat /data/database/files/000/dataset_609.dat with Input error: found interval with block-counts not matching starts/sizes Where dataset_596.dat is my vcf and /data/database/files/000/dataset_598.dat is my genome file. This is produced by the bedtools genomecov bit of the command, which appears to have some sort of problem with the vcf input in combination with the -split option. The problem disappears with the installation of the latest version of bedtools (v2.17.0), but if you are using the version that you get from yum (v2.15.0) you run into this error. Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Visualisation of VCF files in trackster
Dear Jeremy Thank you for your reply and sorry for not being clear. In short I solved the problem. Below is some info, in case this is useful for someone else. Thanks for your help The situation was: On Main: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - OK On my local install: Visualisation of the SAM/BAM file - OK Visualisation of the VCF file - FAIL The reason is that this command fails: grep -v '^#' /data/database/files/000/dataset_596.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /data/database/files/000/dataset_598.dat temp.bg ; bedGraphToBigWig temp.bg /data/database/files/000/dataset_598.dat /data/database/files/000/dataset_609.dat with Input error: found interval with block-counts not matching starts/sizes Where dataset_596.dat is my vcf and /data/database/files/000/dataset_598.dat is my genome file. This is produced by the bedtools genomecov bit of the command, which appears to have some sort of problem with the vcf input in combination with the -split option. The problem disappears with the installation of the latest version of bedtools (v2.17.0), but if you are using the version that you get from yum (v2.15.0) you run into this error. Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Visualisation of VCF files in trackster
Dear all My attempts to visualise a vcf file in trackster fail. I can visualise the corresponding SAM/BAM files fine. I can visualise the same file on Galaxy main too, but not in my local install. I receive the following error message: Trackster Error Input error: found interval with block-counts not matching starts/sizes on line. sort: write failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 1000) The vcf format is in version 4.1. I am creating it from the sorted BAM file with samtools mpileup in the most basic way. What am I missing? Thanks a lot for your help Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Visualisation of VCF files in trackster
My attempts to visualise a vcf file in trackster fail. I can visualise the corresponding SAM/BAM files fine. I can visualise the same file on Galaxy main too, but not in my local install. To be clear, you can visualize the VCF dataaset on main but not locally? Can you visualize SAM/BAM datasets locally? One guess is that you may need to install and add tabix and bgzip to your path. J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
