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Old 07-17-2012, 07:48 AM   #1
bioman1
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Default tblastx error-ncbi-blast-2.2.26+

Hello all,
I am using ncbi-blast-2.2.26+ version on Linux machine (64 bit) with Fedora 16 OS. I have tried tblastx with my local nucleotide database
against ensembl fish cDNA sequence. I have followed these steps

1.makeblastdb -in example.fa -dbtype nucl -out example_nucl -logfile example_nuclblast.log

2.tblastx -db example_nucl -query fish.fa -out tblastx_result.tsv -max_target_seqs 20 -evalue 1e-10 -outfmt "7 qseqid sseqid pident length mismatch gaps qstart qend sstart send sqlen slen evalue bitscore" -num_threads 32

I get error

Error: NCBI C++ Exception:
"/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_1540_130.14.18.6_9051_1329940081/rpmbuild/BUILD/ncbi-blast-2.2.26+/c++/src/objtools/alnmgr/alnmap.cpp", line 733: Error: CAlnVec::x_GetSeqLeftSeg(): Invalid Dense-seg: Row 0 contains gaps only.


Can you tell me why tblastx creating error. It outputs file but stops in between.

I tried looking source file at line no 00733

http://0-www.ncbi.nlm.nih.gov.ilspro...pp_source.html

Any help is appreciated
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Old 07-20-2012, 03:47 AM   #2
maubp
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It looks like a bug - please report this to the NCBI BLAST team via the email address on their webpage, blast-help (at) ncbi.nlm.nih.gov
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Old 01-13-2013, 04:45 PM   #3
AdrianP
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happens to me too, no idea why. they went to next ver and still it happens.
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Old 01-13-2013, 05:24 PM   #4
maubp
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Perhaps bioman1 didn't report the bug, in which case it is hardly surprising the NCBI haven't fixed it. Could you (also) report the bug - a simple reproducible example would be ideal.
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Old 01-13-2013, 05:47 PM   #5
AdrianP
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it will be complicated to give a simple example, since I got no idea where the problem in my query fasta file is. I will be able to report this bug only after my data can be made publicly available... I too am using Fedora, so it seems this is either a redhat bug, or fedora only.
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Old 01-16-2013, 06:57 AM   #6
dnusol
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I am not sure, but how about using formatdb instead of makeblastdb?

HTH

Edit: formatdb is discontinuated but I have used it recently with apparently no errors when running blast 2.26+

Last edited by dnusol; 01-17-2013 at 03:34 AM.
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Old 02-12-2013, 05:07 PM   #7
pschwien
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Hey, I've encountered this error if one of the input files is not readable (in my case I invoked the tblastx in a wrong directory and the relative paths to the files were wrong).

Hope that helps.
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Old 02-13-2013, 06:04 AM   #8
maubp
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Hi pschwien, that information should be very useful to the NCBI BLAST+ team - please email them about this (since they don't have a public bug tracker).
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