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

[Carson Holt]

You set TMP=makertmp. That is likly not a true locally mounted location (i.e. it’s network mounted). In which case you will hit a race condition where files you just created don’t become readable for a few milliseconds to seconds after creation under heavy IO load. Alternatively it is locally mounted, but only exists on a single node and you are running it on a cluster (other nodes cannot cross access local nodes).

Unless your cluster setup has a specific location for locally mounted temporary scratch space, you should not set TMP=. Just let it default to /tmp which is almost always locally mounted.

—Carson


> On Jan 25, 2018, at 3:26 AM, Marni Tausen <marni at cs.au.dk> wrote:
> 
> 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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