[maker-devel] Strange error at blastn step

[Mark Yandell]

Hi Daniel,

I think its your fasta-file

'> comp59088_c1_seq' note the space between the chevron and the id. This isn't allowed by the fasta format. 

cheers,

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [daniel.standage at gmail.com]
Sent: Friday, October 26, 2012 11:52 AM
To: Maker Mailing List
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<mailto: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