[maker-devel] Strange error at blastn step

Fri Oct 26 12:12:38 MDT 2012

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.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.output/maker.bogus_datastore/scaffold_866/theVoid.scaff
>>> old_866/scaffold_866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrimmomatic%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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>>
>
>
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