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

[Marcelo Luiz de Laia]

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 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