[maker-devel] Strange error at blastn step

Fri Oct 26 12:14:29 MDT 2012

The command 'df /tmp' will tell you whether /tmp is a tmpfs mount

Thanks,
Carson

From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Friday, 26 October, 2012 2:12 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Strange error at blastn step

It looks like /tmp is indeed being used: the files I played with were under
/tmp/maker_1YQF9o.

--
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 2:09 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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.make
>>> r.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.m
>>> pi.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.make
>>> r.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.m
>>> pi.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%2Efast
>>>> a.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.ou
>>>> tput/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold_866.0
>>>> .Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrim
>>>> momatic%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
>>> 
>> 
>> _______________________________________________ maker-devel mailing list
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>> ker-devel_yandell-lab.org
> 

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