[maker-devel] install maker on cluster
Carson Holt
carsonhh at gmail.com
Tue Oct 16 09:18:48 MDT 2012
Delete any file in the maker output directory that start with the name
.init or .NFS then rerun.
Thanks,
Carson
On 12-10-16 11:14 AM, "Christoph Hahn" <chrisi.hahni at gmail.com> wrote:
>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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