Trouble using custom repeat library w/ Maker v2.31.10

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Trouble using custom repeat library w/ Maker v2.31.10

Martin, John
Greetings,

     I'm trying to use a custom repeat library in a maker run being
performed on a ~400Mb worm genome.   I've successfully tested my
installation of maker v2.31.10 using a small set of 13 contigs from my
full assembly (~100kb or less) using the 'model_org=all' setting for the
RepeatMasker part of the maker_opts.ctl configuration.  But when I try
to feed maker my repeat library fasta file, maker errors out when trying
to repeatmask because its trying to run hmmpress on the fasta file I set
as 'rmlib=...'

     I've attached the 3 .ctl files I'm using.  I am not setting any
other command line arguments for maker, when I launch the jobs I just type:

maker

in the directory with those .ctl files.   The specific error message I
am getting appears inside each of the subdirectories of the datastore,
inside hmmPress.log files:

Error: File format problem in trying to open HMM file
/gscmnt/gc2732/mitrevalab/
USDA_Zarlenga/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/
SUPERNOVA_assembly/ANNOTATION/MAKER/maker_1/TMP_1/maker_sbWsNX/RM_416.MonJul1522
04492019/consensi.fa.classified.
Format tag is '>rnd-1_family-14#Unknown': unrecognized.
Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.

I am not sure why maker is trying to run hmmpress on the fasta file
entered for the 'rmlib' setting, which the documentation says should be
fasta.   I think hmmpress should be used on hmm files. Can someone help
me troubleshoot this problem?


Thanks,

John Martin


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Re: Trouble using custom repeat library w/ Maker v2.31.10

Carson Holt-2
Reinstall RepeatMasker Manually. It’s apparently been configured during it’s install to use HMMER, and it’s possible that it was done incorrectly if it was done by a package manager like homebrew.

It’s installed under /usr/local/RepeatMasker/ according to your maker_exe.ctl file.

—Carson



> On Jul 15, 2019, at 6:58 PM, Martin, John <[hidden email]> wrote:
>
> Greetings,
>
>     I'm trying to use a custom repeat library in a maker run being
> performed on a ~400Mb worm genome.   I've successfully tested my
> installation of maker v2.31.10 using a small set of 13 contigs from my
> full assembly (~100kb or less) using the 'model_org=all' setting for the
> RepeatMasker part of the maker_opts.ctl configuration.  But when I try
> to feed maker my repeat library fasta file, maker errors out when trying
> to repeatmask because its trying to run hmmpress on the fasta file I set
> as 'rmlib=...'
>
>     I've attached the 3 .ctl files I'm using.  I am not setting any
> other command line arguments for maker, when I launch the jobs I just type:
>
> maker
>
> in the directory with those .ctl files.   The specific error message I
> am getting appears inside each of the subdirectories of the datastore,
> inside hmmPress.log files:
>
> Error: File format problem in trying to open HMM file
> /gscmnt/gc2732/mitrevalab/
> USDA_Zarlenga/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/
> SUPERNOVA_assembly/ANNOTATION/MAKER/maker_1/TMP_1/maker_sbWsNX/RM_416.MonJul1522
> 04492019/consensi.fa.classified.
> Format tag is '>rnd-1_family-14#Unknown': unrecognized.
> Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.
>
> I am not sure why maker is trying to run hmmpress on the fasta file
> entered for the 'rmlib' setting, which the documentation says should be
> fasta.   I think hmmpress should be used on hmm files. Can someone help
> me troubleshoot this problem?
>
>
> Thanks,
>
> John Martin
>
>
> ________________________________
> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
> <maker_bopts.ctl><maker_opts.ctl><maker_exe.ctl>_______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Trouble using custom repeat library w/ Maker v2.31.10

Martin, John
Thanks Carson, I actually had a second, older installation of
RepeatMasker that defaulted to wu-blast that I was able to use (by
modifying maker_exe.ctl to point to it) and that looks like it fixed my
problem.


John




On 7/16/19 2:51 PM, Carson Holt wrote:

> Reinstall RepeatMasker Manually. It’s apparently been configured during it’s install to use HMMER, and it’s possible that it was done incorrectly if it was done by a package manager like homebrew.
>
> It’s installed under /usr/local/RepeatMasker/ according to your maker_exe.ctl file.
>
> —Carson
>
>
>
>> On Jul 15, 2019, at 6:58 PM, Martin, John <[hidden email]> wrote:
>>
>> Greetings,
>>
>>      I'm trying to use a custom repeat library in a maker run being
>> performed on a ~400Mb worm genome.   I've successfully tested my
>> installation of maker v2.31.10 using a small set of 13 contigs from my
>> full assembly (~100kb or less) using the 'model_org=all' setting for the
>> RepeatMasker part of the maker_opts.ctl configuration.  But when I try
>> to feed maker my repeat library fasta file, maker errors out when trying
>> to repeatmask because its trying to run hmmpress on the fasta file I set
>> as 'rmlib=...'
>>
>>      I've attached the 3 .ctl files I'm using.  I am not setting any
>> other command line arguments for maker, when I launch the jobs I just type:
>>
>> maker
>>
>> in the directory with those .ctl files.   The specific error message I
>> am getting appears inside each of the subdirectories of the datastore,
>> inside hmmPress.log files:
>>
>> Error: File format problem in trying to open HMM file
>> /gscmnt/gc2732/mitrevalab/
>> USDA_Zarlenga/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/
>> SUPERNOVA_assembly/ANNOTATION/MAKER/maker_1/TMP_1/maker_sbWsNX/RM_416.MonJul1522
>> 04492019/consensi.fa.classified.
>> Format tag is '>rnd-1_family-14#Unknown': unrecognized.
>> Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.
>>
>> I am not sure why maker is trying to run hmmpress on the fasta file
>> entered for the 'rmlib' setting, which the documentation says should be
>> fasta.   I think hmmpress should be used on hmm files. Can someone help
>> me troubleshoot this problem?
>>
>>
>> Thanks,
>>
>> John Martin
>>
>>
>> ________________________________
>> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>> <maker_bopts.ctl><maker_opts.ctl><maker_exe.ctl>_______________________________________________
>> maker-devel mailing list
>> [hidden email]
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org