[maker-devel] Strange error at blastn step

Fri Oct 26 12:09:39 MDT 2012

Check to see where /tmp is located?  Some clusters have it set up as a tmpfs
directory and I have had problems with fasta indexes running from tmpfs
mounts in the past.

--Carson

From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Friday, 26 October, 2012 2:05 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Strange error at blastn step

The maker working directory is in a cluster environment with shared scratch
space (I'm guessing NFS-mounted). I didn't change the temp directory
setting, so it should be the local default (/tmp).

I'll give the dev version a shot. Thanks.

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University

On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Could you try this development version and tell me if the error still happens?
> 
> Use this command to download -->
> <<blanked out from the mailing list>>
> 
> Username: <<blanked out from the mailing list>>
> Password: <<blanked out from the mailing list>>
> 
> Are you running in an NFS mounted directory or are you resetting TMP to a
> different location?
> 
> Thanks,
> Carson
> 
> 
> From:  Daniel Standage <daniel.standage at gmail.com>
> Date:  Friday, 26 October, 2012 1:52 PM
> To:  Maker Mailing List <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Strange error at blastn step
> 
> I have since installed Maker on a different machine and tried it out. The test
> run completed successfully, but as I commenced with the full genome
> annotation, I have noticed the following error popping up frequently.
> 
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8
>> #-------------------------------#
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /N/u/dstandag/Mason/local/bin/blastx -db
>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query
>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 -num_descriptions
>> 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 16 -seg yes
>> -soft_masking true -lcase_masking -show_gis -out
>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker
>> .output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0
>> .0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.
>> 10.8.blastx
>> #-------------------------------#
>> deleted:-10 hits
>> formating database...
>> #--------- command -------------#
>> Widget::formater:
>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in
>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9
>> #-------------------------------#
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /N/u/dstandag/Mason/local/bin/blastx -db
>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query
>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 -num_descriptions
>> 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 16 -seg yes
>> -soft_masking true -lcase_masking -show_gis -out
>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker
>> .output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0
>> .0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.
>> 10.9.blastx
>> #-------------------------------#
>> deleted:-6 hits
>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta.
>> stop here:comp59088_c1_seq7
>> ERROR: Fasta index error
>> 
>> FATAL ERROR
>> ERROR: Failed while polishig ESTs!!
>> 
>> ERROR: Chunk failed at level 14
>> !!
>> FAILED CONTIG:scaffold_0
>> 
>> 
>> 
>> 
>> --Next Contig--
>> 
>> #---------------------------------------------------------------------
>> Now starting the contig!!
>> SeqID: scaffold_1
>> Length: 5805686
>> #---------------------------------------------------------------------
> 
> My first thought based on the message is that blastdbcmd could not find the
> sequence in the database. I verified this was the case--I could not extract
> sequence comp59088_c1_seq7 from the database Maker had created under /tmp.
> However, after removing the index files and re-running makeblastdb with the
> -parse_seqids option set, blastdbcmd successfully extracted the sequence.
> 
> I was initially happy with this finding, but upon closer inspection it looks
> like Maker does not use blastdbcmd to extract sequences, but rather its own
> internal code. Therefore I'm still not sure where the problem is and how I
> might fix it. Any insights?
> 
> Thanks!
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
> 
> 
> 
> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage <daniel.standage at gmail.com>
> wrote:
>> Greetings!
>> 
>> I am doing a test run of my Maker setup on a new machine, annotating a pretty
>> short contig (about 3kb). However, there seems to be a hiccup during the
>> blastn stage. This is the terminal message.
>> 
>>> #--------- command -------------#
>>> Widget::blastn:
>>> /share/home/01854/standage/local/bin/blastn -db
>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Efasta
>>> .mpi.10.7 -query
>>> /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 -num_alignments
>>> 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend 3 -word_size 15
>>> -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp 500000000
>>> -num_threads 16 -lcase_masking -dust yes -soft_masking true -show_gis -out
>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker.out
>>> put/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold_866.0.P
>>> dom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrimmom
>>> atic%2Efasta.mpi.10.7.blastn
>>> #-------------------------------#
>>> deleted:0 hits
>>> ERROR:  Could not obtain lock to format database
>>> 
>>> 
>>> FATAL ERROR
>>> ERROR: Failed while doing blastn of ESTs!!
>>> 
>>> ERROR: Chunk failed at level 8
>>> !!
>>> FAILED CONTIG:scaffold_866
>> 
>> Several blastn steps appeared to have completed successfully to this one
>> failing. Any ideas what could be causing this?
>> 
>> Thanks!
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Bioinformatics and Computational Biology Program
>> Department of Genetics, Development, and Cell Biology
>> Iowa State University
>> 
> 
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