Maker run problems - BLAST makeblastdb failed

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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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Re: Maker run problems - BLAST makeblastdb failed

Martin MOKREJŠ
Hi Marni,
  do not use spaces in your filenames and directory names. I think that is your issue: te_proteins%2Efasta.mpi.10.0

Martin

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Re: Maker run problems - BLAST makeblastdb failed

Carson Holt-2
In reply to this post by Marni Tausen
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 <[hidden email]> 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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[hidden email]
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