Re: [galaxy-dev] TopHat error
Hello, I would start by confirming the SAMTools indexes and tool installs. Confirm that you can execute SAMTools tool's successfully within Galaxy. If there are problems, check to see if there is a PATH issue. Make sure the galaxy user is accessing the correct version (and indexes for reference genomes used). If you are using a cluster, then confirm the tools/indexes are configured correctly there, too. Hopefully this helps, Jen Galaxy team On Mon, Mar 9, 2015 at 8:08 AM, Scott Szakonyi scott.b.szakony...@nd.edu wrote: Hello all, I have a user who is getting the following error when analyzing a FASTQ file using TopHat for Illumina. TopHat v2.0.10 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header. [bam_index_build2] fail to index the BAM file. Error indexin I've tried reloading the tool and all it's dependencies, to no avail. We've been able to run the same FASTQ file successfully on another Galaxy server with identical tool configuration. I'm out of ideas, being relatively new to Galaxy. Has anyone seen a similar error? Can you offer an possible solutions? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon mike.t...@gmail.com wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary. Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place... I can see your chain of thought here. Unfortunately while the tophat tool (or any tool) may explicitly use samtools (and request a particular version via the dependencies system), once the tool has finished it has produced a BAM file. So far so good, but at that point Galaxy tries to index the BAM file itself. This happens for any BAM file, regardless of the tool which created it - and simply expects samtools on the $PATH. If this is on the wiki (core dependencies of Galaxy itself), could someone post the URL here please? Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Am 24.02.2015 um 10:03 schrieb Peter Cock: ... So far so good, but at that point Galaxy tries to index the BAM file itself. This happens for any BAM file, regardless of the tool which created it - and simply expects samtools on the $PATH. If this is on the wiki (core dependencies of Galaxy itself), could someone post the URL here please? It is not listed here: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList Yes, that page is about dependencies of add-on tools (things that existing or new tools may assume are installed). In this case samtools is expected by the Galaxy core (not a tool). What else falls into this set of dependencies? I can be wrong but I think Galaxy will search in galaxy-tools/samtools/default if samtools is not on your $PATH. Can anyone confirm this? Ciao, Bjoern I don't know, sorry. Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
Am 24.02.2015 um 10:03 schrieb Peter Cock: On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon mike.t...@gmail.com wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary. Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place... I can see your chain of thought here. Unfortunately while the tophat tool (or any tool) may explicitly use samtools (and request a particular version via the dependencies system), once the tool has finished it has produced a BAM file. So far so good, but at that point Galaxy tries to index the BAM file itself. This happens for any BAM file, regardless of the tool which created it - and simply expects samtools on the $PATH. If this is on the wiki (core dependencies of Galaxy itself), could someone post the URL here please? It is not listed here: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList I can be wrong but I think Galaxy will search in galaxy-tools/samtools/default if samtools is not on your $PATH. Can anyone confirm this? Ciao, Bjoern Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
Am 24.02.2015 um 13:01 schrieb Nicola Soranzo: Il 24.02.2015 10:19 Björn Grüning ha scritto: Am 24.02.2015 um 10:03 schrieb Peter Cock: On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary. Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place... I can see your chain of thought here. Unfortunately while the tophat tool (or any tool) may explicitly use samtools (and request a particular version via the dependencies system), once the tool has finished it has produced a BAM file. So far so good, but at that point Galaxy tries to index the BAM file itself. This happens for any BAM file, regardless of the tool which created it - and simply expects samtools on the $PATH. If this is on the wiki (core dependencies of Galaxy itself), could someone post the URL here please? It is not listed here: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList I can be wrong but I think Galaxy will search in/samtools/default if samtools is not on your $PATH. Can anyone confirm this? Galaxy should search first in tool_dependencies_dir/samtools/default/ (where tool_dependencies_dir is what you have configured in the tool_dependency_dir directive of config/galaxy.ini), then in $PATH . Great thanks Nicola! Bjoern Best, Nicola Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
Hi - Thanks for the info. I had two versions of samtools installed so I uninstalled one and left only samtools 0.1.19 however I still get the error. I'm using the tophat2 tool and I'm still getting the error. I just reinstalled the tophat2 tool and I'm running it again. On Feb 23, 2015, at 8:23 AM, Saket Choudhary sake...@gmail.com wrote: On 22 February 2015 at 23:17, Michael Thon mike.t...@gmail.com wrote: bam_index_build2() not yet Hi Michael, This seems to be related to this: https://github.com/samtools/samtools/issues/199 You should probably switch to samtools 0.1.19 Saket ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
On Feb 23, 2015, at 8:23 AM, Saket Choudhary sake...@gmail.com wrote: On 22 February 2015 at 23:17, Michael Thon mike.t...@gmail.com wrote: bam_index_build2() not yet Hi Michael, This seems to be related to this: https://github.com/samtools/samtools/issues/199 You should probably switch to samtools 0.1.19 Saket I figured that galaxy must be finding a samtools v1.1 even though the tool was not installed, according to the admin page. I uninstalled the samtools that was installed system-wide on the server. Now I get this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1107, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 250, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found So, galaxy is not using the samtools from the installed galaxy package and is instead using the system one. I'll try to reinstall samtools and see if that fixes it... ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tophat error
The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that tophat has a dependency on samtools of type package and I assumed that should provide the samtools binary. Of course I have not read the manuals regarding tool sheds, dependencies, etc so thats probably where my problem started in the first place... On Feb 24, 2015, at 3:18 AM, John Chilton jmchil...@gmail.com wrote: Sorry for this messy situation. With the next release Galaxy will be able to set metadata using any version of samtools due to an excellent fix by Nate - so this hopefully will become less of an issue. -John On Mon, Feb 23, 2015 at 10:01 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon mike.t...@gmail.com wrote: I figured that galaxy must be finding a samtools v1.1 even though the tool was not installed, according to the admin page. I uninstalled the samtools that was installed system-wide on the server. Now I get this error: Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1107, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 250, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found So, galaxy is not using the samtools from the installed galaxy package and is instead using the system one. I'll try to reinstall samtools and see if that fixes it... In this case Galaxy itself expects samtools on the $PATH for managing BAM files separately from which ever tool you are using within Galaxy. The Galaxy Tool Shed dependencies are on a per-tool basis, and not used by Galaxy itself. This ought to be on the wiki somewhere, but I failed to find it... Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
