[maker-devel] Maker run problems - BLAST makeblastdb failed

[Marni Tausen]

Hey,

I have a problem getting maker to run.

I’ve tried installing the pipeline on three separate systems. CentOS 6 (cluster), Mac OS X 10.12.6 and on CentOS 7.

With each of them I run into problems with Repeatmasker step with the error message:

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: chr0
Length: 38046352
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd makertmp/maker_DMTHbJ; /Users/PM/maker/exe/RepeatMasker/RepeatMasker /Users/PM/GENEANNOTATION/TrR.v5.maker.output/TrR.v5_datastore/82/7E/chr0//theVoid.chr0/0/chr0.0.all.rb -species all -dir /Users/PM/GENEANNOTATION/TrR.v5.maker.output/TrR.v5_datastore/82/7E/chr0//theVoid.chr0/0 -pa 1
#-------------------------------#
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/Users/PM/maker/bin/../exe/lblast/bin/makeblastdb -dbtype prot -in makertmp/maker_DMTHbJ/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
BLAST options error: File makertmp/maker_DMTHbJ/0/blastprep/te_proteins%2Efasta.mpi.10.0 does not exist
ERROR: /Users/PM/maker/bin/../exe/lblast/bin/makeblastdb failed in Widget::formater
--> rank=NA, hostname=d24834.local
ERROR: Failed while doing blastx repeats
ERROR: Chunk failed at level:1, tier_type:1
FAILED CONTIG:chr0

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:chr0

examining contents of the fasta file and run log

The Maker version that was installed is 2.31.9, and it was build using the ./Build commands.

However the links for exonerate (2.2.0) and repeatmasker (repbase) (latest version) seem to be broken, as they always returned connection errors.

So I manually installed both of those programs and linked maker to them.

I’ve attached the config files and the script used to run maker.

Cheers,
Marni Tausen


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