Control: forwarded -1 https://github.com/bbuchfink/diamond/issues/351
Hi Marcelo, thank you for the effort you have spent into this issue. I' watching the upstream issue and due to the first line in this mail also the Debian Bug Tracking system will do so. On Tue, May 19, 2020 at 08:19:44AM -0300, Marcelo Luiz de Laia wrote: > Package: diamond-aligner > Version: 0.9.32-2 > Severity: important > > Dear Maintainer, > > I run diamond like this: > > diamond blastx --threads 2 --outfmt 5 --max-target-seqs 5 --evalue 1e-5 --db > /home/marcelo/Diamond_DB/nr --query /home/marcelo/Google\ > Drive/Mlaia/NoISeq/ExonID_GDE.fa -o /home/marcelo/Google\ > Drive/Mlaia/Blastn/blastx.exons.diamond.xml > > And I got this error: > > marcelo@marcelo:~/Google Drive/Mlaia/Blastn$ diamond blastx --outfmt 5 --max- > target-seqs 5 --evalue 1e-5 --db /media/marcelo/Seagate\ Expansion\ > Drive/NCBI_DB/Diamond/nr --query /home/marcelo/Google\ > Drive/Mlaia/NoISeq/ExonID_GDE.fa -o /home/marcelo/Google\ > Drive/Mlaia/Blastn/blastx.exons.diamond.xml > diamond v0.9.32.133 (C) Max Planck Society for the Advancement of Science > Documentation, support and updates available at http://www.diamondsearch.org > > #CPU threads: 4 > Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) > Temporary directory: /home/marcelo/Google Drive/Mlaia/Blastn > Opening the database... [0s] > #Target sequences to report alignments for: 5 > Reference = /media/marcelo/Seagate Expansion Drive/NCBI_DB/Diamond/nr.dmnd > Sequences = 282858011 > Letters = 101765175729 > Block size = 2000000000 > Opening the input file... [0s] > Opening the output file... [0s] > Loading query sequences... [0.046s] > Masking queries... diamond: /build/diamond-aligner-jUHUMq/diamond- > aligner-0.9.32/src/lib/Eigen/src/Core/DenseCoeffsBase.h:408: > Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, > 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; > Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: > Assertion `index >= 0 && index < size()' failed. > diamond: /build/diamond-aligner-jUHUMq/diamond- > aligner-0.9.32/src/lib/Eigen/src/Core/DenseCoeffsBase.h:408: > Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, > 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; > Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: > Assertion `index >= 0 && index < size()' failed. > Abortado (Nice, "Abortado" sounds way more kind than "Aborted" ;-)) ) > marcelo@marcelo:~/Google Drive/Mlaia/Blastn$ > > I opened a issue on diamond support forum at > https://github.com/bbuchfink/diamond/issues/351 > > Please, could you see that thread? May be this bug is only in the Debian > version, because I run the github version 0.32 and it worked out of the box. Thanks a lot. That's very helpful information. Same question as inside the github issue: Are you able to provide the dataset you have used? Additional question: Does the call work with *other* datasets you might have used? We try to debug the issue and for sure the Debian packaged version should provide the same results the code that is fetched from upstream. We should definitely add this somehow in an autopkgtest. One quick idea came up that we might link against Debian packaged libeigen - but when checking this is actually not the case. This is bad Debian policy wise but at least for the case of debugging this issue its good to work on the very same code basis. Kind regards Andreas. -- http://fam-tille.de
