[maker-devel] 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 <jmartin at wustl.edu> 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
>>
>>
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