Public bug reported: On ubuntu 20.04.2, ncbi-blast+ 2.9.0-2
It appears that the parsing logic in the script was broken by the ncbi entrez api at some point. When running this script with -n [species], it returns the number of results and no more. Running the script included with the latest version, 2.12.0, functions correctly with its modified parsing. Best way to resolve this is likely to just put the 2.12.0 script in the package. Attached. ProblemType: Bug DistroRelease: Ubuntu 20.04 Package: ncbi-blast+ 2.9.0-2 ProcVersionSignature: Ubuntu 5.8.0-1036.38~20.04.1-azure 5.8.18 Uname: Linux 5.8.0-1036-azure x86_64 ApportVersion: 2.20.11-0ubuntu27.18 Architecture: amd64 CasperMD5CheckResult: pass Date: Thu Jul 1 20:15:40 2021 InstallationDate: Installed on 2021-06-29 (1 days ago) InstallationMedia: Ubuntu-Server 20.04.2 LTS "Focal Fossa" - Release amd64 (20210201.2) ProcEnviron: SHELL=/bin/bash LANG=en_US.UTF-8 TERM=xterm-256color XDG_RUNTIME_DIR=<set> PATH=(custom, no user) SourcePackage: ncbi-blast+ UpgradeStatus: No upgrade log present (probably fresh install) ** Affects: ncbi-blast+ (Ubuntu) Importance: Undecided Status: New ** Tags: amd64 apport-bug focal patch uec-images ** Patch added: "script from 2.12.0" https://bugs.launchpad.net/bugs/1934402/+attachment/5508502/+files/get_species_taxids.sh -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1934402 Title: get_species_taxids does not print all information when invoked with -n To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/1934402/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs