[Debian-med-packaging] Bug#961013: Bug#961013: diamond-aligner: Diamond faill with the error: Assertion `index >= 0 && index < size()' failed.

[olivier sallou]

On Tue, 2020-05-19 at 08:19 -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:

did not tried with blastx but debian has some autotests on blastp (and
tried on a fresh install with example files) and faced no issue with
diamond.

example: diamond blastp --threads 1 --db 'M.faa.diamond' --query
'L.faa' --out L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6  --sensitive

diamond has no dependency on other debian libs, so it cannot be an
issue with an external lib being too old (or recent).

as package is built based on git release tag, code should be the same,
so is very difficult to debug (without knowing code itself).

compilation issue?

Olivier
> 
> marcelo at 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
> marcelo at 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.
> 
> Thank you.
> 
> 
> 
> -- System Information:
> Debian Release: bullseye/sid
>   APT prefers testing
>   APT policy: (990, 'testing'), (500, 'stable'), (250, 'unstable'),
> (50, 'experimental')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
> 
> Kernel: Linux 5.6.0-1-amd64 (SMP w/4 CPU cores)
> Kernel taint flags: TAINT_CRAP, TAINT_OOT_MODULE,
> TAINT_UNSIGNED_MODULE
> Locale: LANG=pt_BR.UTF-8, LC_CTYPE=pt_BR.UTF-8 (charmap=UTF-8),
> LANGUAGE=pt_BR:pt:en (charmap=UTF-8)
> Shell: /bin/sh linked to /usr/bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
> 
> Versions of packages diamond-aligner depends on:
> ii  libc6       2.30-7
> ii  libgcc-s1   10.1.0-1
> ii  libstdc++6  10.1.0-1
> ii  zlib1g      1:1.2.11.dfsg-2
> 
> Versions of packages diamond-aligner recommends:
> ii  med-config  3.5.1
> 
> diamond-aligner suggests no packages.
> 
> -- no debconf information
> 
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-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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