Your message dated Mon, 31 Aug 2020 16:11:47 +0200
with message-id
<CAD=WrcJSEU0Vsgh1_Uv0ky8Cn_FqfNTxzAMSbtNUPsk=hd7...@mail.gmail.com>
and subject line upstream's fix is in the Debian archive
has caused the Debian Bug report #961013,
regarding diamond-aligner: Diamond faill with the error: Assertion `index >= 0
&& index < size()' failed.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
961013: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961013
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
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.
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
--- End Message ---
--- Begin Message ---
Version: 2.0.4-1
The release with the fixed version has made its way into Debian. Thanks
again to Pranav for narrowing down the problem so upstream could fix it!
--- End Message ---
