[maker-devel] Strange error at blastn step

Fri Oct 26 14:49:57 MDT 2012

Right but is tmp on a disk or a tmpfs 
 df -h /tmp 
would give you the first hint at whether it is a local drive or something else.

On Oct 26, 2012, at 11:12 AM, Daniel Standage <daniel.standage at gmail.com> wrote:

> 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.scaffold_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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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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