[maker-devel] install maker on cluster
Christoph Hahn
chrisi.hahni at gmail.com
Tue Oct 16 10:12:21 MDT 2012
The maker output directory contains only one thing:
.NFSLock.init_lock.NFSLock, which is a link to
.NFSLock.init_lock.tmp.3358.21603.1715.48578929183 in the same directory.
When I delete it and rerun maker I get the same error and another
.NFSLock.init_lock.NFSLock is created, this one is linked to
.NFSLock.init_lock.tmp.3635.21981.7756.8294996771
Thanks,
Christoph
Am 16.10.2012 17:18, schrieb Carson Holt:
> 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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