[maker-devel] Strange error at blastn step

Fri Oct 26 12:20:55 MDT 2012

Running 2.10.

--
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 2:19 PM, Barry Moore
<barry.moore at genetics.utah.edu>wrote:

> Hi Daniel,
>
> What version or revision of MAKER are you running.  This sounds like
> something we were seeing here last night.  We traced it as far as what
> appeared to be soft links in /tmp being set incorrectly.  The FastaDB
> objects had pointers to fasta files in the void for the correct fasta file,
> but their dir attribute pointed to a /tmp directory in where there were
> soft links to another (incorrect)  fasta file with it's index.  It would
> look appeared that it was looking in the /tmp index (which pointed to an
> incorrect fasta file) and when it failed to find what it was looking for it
> would re-index the fasta file in the void (the correct one) and then look
> again in the index in tmp.  Don't know if that helps, but the errors look
> similar and that's as far as I got with our error here…  This was on one of
> Mike's annotation projects, so I don't know for sure what revision he was
> running, but I think it was the latest.
>
> B
>
> On Oct 26, 2012, at 11:52 AM, Daniel Standage wrote:
>
> 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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>
>
>  Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
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