[maker-devel] 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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