[maker-devel] install maker on cluster
Christoph Hahn
chrisi.hahni at gmail.com
Tue Oct 16 09:14:36 MDT 2012
Hi Carson,
It was a link. The path was not correct any more because of the
migration to the new cluster. I could not change it so I just gave the
path to the real file in the maker_opts file. That has resolved this
error, but now I am getting the following:
STATUS: Parsing control files...
ERROR: Cannot get initialization lock.
Probably not relevant any more, but: No trailing commas, no ':'
characters in the path.
Thanks for your help!
Christoph
Am 16.10.2012 16:19, schrieb Carson Holt:
> No. that's just a recommendation for the maker2chado script to work.
>
> Is es.mod the actual HMM or a soft link to the HMM?
> After the error message their should be a list of the actual files. Does
> it print that?
> Are there trailing commas in you maker_opts.ctl file after the hmm file
> name in the control files?
> Are their ':' characters in the path name to the file?
>
> --Carson
>
>
>
> On 12-10-16 10:02 AM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:
>
>> Thanks for your help Carson!
>>
>> I tried maker2.26, but the error still remains. I also tried to change
>> the TMP= option in the maker_opts file, but no change either..
>>
>> STATUS: Parsing control files...
>> ERROR: The HMM file[s] provided for gmhmm do not exist:
>>
>> When building the maker2.26 I saw that it is complaining about one more
>> (recommended) dependency (I must have overlooked that before):
>> Checking prerequisites...
>> recommends:
>> * DBD::Pg is not installed
>>
>> I am having problems to get that one.. Is that causing the error?
>>
>> much obliged,
>> Christoph
>>
>> Am 15.10.2012 20:05, schrieb Carson Holt:
>>> It looks like either an NFS issue or perhaps an issue with the location
>>> provided for the TMP= in the maker_opts.ctl file.
>>>
>>> First I would suggest trying maker 2.26 to see if the issue still
>>> happens
>>> there (there are a few updates to how NFS locks are handled in 2.26).
>>>
>>> Second if you are setting TMP make sure your disk is not full. Or if
>>> TMP
>>> was set to a tmpfs location (in memory filesystem), it could be a full
>>> memory issue in which case you could just set TMP to somewhere else.
>>>
>>> Let me know if you still see the issue in 2.26 or after changing the
>>> location of TMP.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> On 12-10-12 1:09 PM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:
>>>
>>>> Hi Carson,
>>>>
>>>> Thanks for your reply. I managed to install maker2.25 properly now, but
>>>> when running it I am getting strange errors (two kinds):
>>>> type one:
>>>> STATUS: Parsing control files...
>>>> ERROR: The HMM file[s] provided for gmhmm do not exist:
>>>>
>>>> type two:
>>>> STATUS: Parsing control files...
>>>> ERROR: Cannot get initialization lock.
>>>>
>>>> I have divided the draft assembly to several files, each containing a
>>>> subset of contigs on which I am running a maker instance. I am getting
>>>> the above named error type one for the majority of the instances,
>>>> although the HMM file it is complaining about (es.mod) is actually in
>>>> the path it is naming (not shown above). In a small number of instances
>>>> I am getting the type two error mentioned above.
>>>>
>>>> Can you help me?
>>>>
>>>> much obliged,
>>>> Christoph
>>>>
>>>>
>>>>
>>>> On 09.10.2012 18:27, Carson Holt wrote:
>>>>> You may need to reconfigure your cpan preferences.
>>>>>
>>>>> You can do this manually by editing the ~/.cpan/CPAN/MyConfig.pm file,
>>>>> or
>>>>> by starting cpan from your command line (command is cpan). Then run
>>>>> 'o
>>>>> conf init' inside the cpan ui.
>>>>>
>>>>> --Carson
>>>>>
>>>>>
>>>>> On 12-10-09 7:07 AM, "Christoph Hahn"<chrisi.hahni at gmail.com> wrote:
>>>>>
>>>>>> Hello maker-team,
>>>>>>
>>>>>> I am trying to install maker 2.25 on a cluster, without root
>>>>>> privileges
>>>>>> (I managed before, but now after migration to a new cluster I cant
>>>>>> seem
>>>>>> to get it to work). All necessary prerequisite programs are installed
>>>>>> and in the path (I followed the steps in the INSTALL file that comes
>>>>>> with maker2.25). When I do: perl Build.PL, I get:
>>>>>> Checking prerequisites...
>>>>>> requires:
>>>>>> ! DBD::SQLite is not installed
>>>>>> ! IO::All is not installed
>>>>>> ! Inline::C is not installed
>>>>>> ! Perl::Unsafe::Signals is not installed
>>>>>> ! Proc::ProcessTable is not installed
>>>>>> ! Want is not installed
>>>>>> ! forks is not installed
>>>>>> ! forks::shared is not installed
>>>>>> build_requires:
>>>>>> ! LWP::Simple is not installed
>>>>>> recommends:
>>>>>> * DBD::Pg is not installed
>>>>>>
>>>>>> ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the
>>>>>> versions
>>>>>> of the modules indicated above before proceeding with this
>>>>>> installation
>>>>>>
>>>>>> Run 'Build installdeps' to install missing prerequisites.
>>>>>>
>>>>>> MAKER supports distributed parallelization via MPI.
>>>>>> Would you like to configure MAKER for MPI (This
>>>>>> requires that you have an MPI client installed)? [N ]n
>>>>>>
>>>>>> WARNING: Apache cannot be located. The optional web based
>>>>>> interface to MAKER will not be available to you.
>>>>>>
>>>>>> Created MYMETA.yml and MYMETA.json
>>>>>> Creating new 'Build' script for 'MAKER' version '2.25'
>>>>>>
>>>>>>
>>>>>> The file 'Build' has been created for you to finish installing MAKER.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> ==
>>>>>> ====
>>>>>> STATUS MAKER 2.25
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> ==
>>>>>> ====
>>>>>> PERL Dependencies: MISSING
>>>>>> ! forks
>>>>>> ! IO::All
>>>>>> ! forks::shared
>>>>>> ! Want
>>>>>> ! DBD::SQLite
>>>>>> ! Proc::ProcessTable
>>>>>> ! Inline::C
>>>>>> ! Perl::Unsafe::Signals
>>>>>>
>>>>>> External Programs: VERIFIED
>>>>>> External C Libraries: VERIFIED
>>>>>> MPI SUPPORT: DISABLED
>>>>>> MWAS Web Interface: DISABLED
>>>>>> MAKER PACKAGE: MISSING PREREQUISITES
>>>>>>
>>>>>>
>>>>>> Important Commands:
>>>>>> ./Build installdeps #installs missing PERL dependencies
>>>>>> ./Build installexes #installs all missing external
>>>>>> programs
>>>>>> ./Build install #installs MAKER
>>>>>> ./Build status #Shows this status menu
>>>>>>
>>>>>> Other Commands:
>>>>>> ./Build repeatmasker #installs RepeatMasker (asks for
>>>>>> RepBase)
>>>>>> ./Build blast #installs BLAST (NCBI BLAST+)
>>>>>> ./Build exonerate #installs Exonerate (v2 on UNIX /
>>>>>> v1
>>>>>> on
>>>>>> Mac OSX)
>>>>>> ./Build snap #installs SNAP
>>>>>> ./Build augustus #installs Augustus
>>>>>> ./Build apollo #installs Apollo
>>>>>> ./Build gbrowse #installs GBrowse (must be root)
>>>>>> ./Build jbrowse #installs JBrowse (MAKER copy, not
>>>>>> web
>>>>>> accecible)
>>>>>> ./Build mpich2 #installs MPICH2 (but manual
>>>>>> install
>>>>>> recommended)
>>>>>>
>>>>>> So it seems some Perl Dependencies are missing. As indicated in
>>>>>> INSTALL
>>>>>> I followed the quick and dirty installation for Bioperl, so I am not
>>>>>> sure what I did wrong/missed out.
>>>>>>
>>>>>> When I run ./Build installdeps, I get:
>>>>>> You do not have write access to install missing Modules.
>>>>>> I can try and install these locally (i.e. only for MAKER)
>>>>>> in the .../maker/perl/lib directory, or you can run
>>>>>> './Build installdeps' as root or using sudo and try again.
>>>>>> Do want MAKER to try and build a local installation? [N ]y
>>>>>> mkdir /usit/titan: Permission denied at
>>>>>> /cluster/software/VERSIONS/perlmodules-5.10_1/lib/perl5/CPAN/FTP.pm
>>>>>> line
>>>>>> 59
>>>>>>
>>>>>> Sorry to bother you with this minor things!! Any help would me much
>>>>>> appreciated!
>>>>>>
>>>>>> much obliged,
>>>>>> Christoph
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>
>
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