Hi, It looks like "ABYSS-P" is missing from the "abyss" package:
root@beluga:~# apt policy abyss abyss: Installed: 2.0.2-3 Candidate: 2.0.2-3 Version table: *** 2.0.2-3 500 500 http://gb.archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages 100 /var/lib/dpkg/status
Using ABYSS-P with MPI is documented on Salsa:
https://salsa.debian.org/med-team/abyss#parallel-processing
Is this a similar Ubuntu problem to "metaphlan2", which is still not in Ubuntu-MATE 18.04 LTS?
AFAIK, Ubuntu 18.04 LTS is based on Debian "buster":
root@beluga:~# cat /etc/debian_version buster/sid
Any ideas how to fix it? Thanks, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis@minke-informatics.co.uk
--- Begin Message ---
- To: "bug-make@gnu.org" <bug-make@gnu.org>
- Cc: Tony Travis <tony.travis@minke-informatics.co.uk>
- Subject: problem with Abyss
- From: Adly Abdalla <adlyhhm@yahoo.com>
- Date: Thu, 14 Feb 2019 11:41:14 +0000 (UTC)
- Message-id: <1422594873.834990.1550144474496@mail.yahoo.com>
- Reply-to: Adly Abdalla <adlyhhm@yahoo.com>
- References: <1422594873.834990.1550144474496.ref@mail.yahoo.com>
Dear Sir/MsI recently installed Abyss assembler through the commandsudo apt-get install abyss
on Ubuntu Mate release 18.04.2 LTS (Bionic Beaver) 64-bit. However when I run Abyss-pe with the small sample data suggested in Githup bcgsc/abyss as default command "abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'" it work fine but when I tried to use Parallel processing with 16 threads using the following command"abyss-pe k=25 np=16 name=test in='test-data/reads1.fastq test-data/reads2.fastq" it failed and gave me this error"adly@bioann:~$ abyss-pe k=25 np=16 name=test in='test-data/reads1.fastq test-data/reads2.fastq'/usr/bin/mpirun -np 16 ABYSS-P -k25 -q3 --coverage-hist=coverage.hist -s test-bubbles.fa -o test-1.fa test-data/reads1.fastq test-data/reads2.fastq--------------------------------------------------------------------------mpirun was unable to find the specified executable file, and thereforedid not launch the job. This error was first reported for processrank 0; it may have occurred for other processes as well.NOTE: A common cause for this error is misspelling a mpirun commandline parameter option (remember that mpirun interprets the firstunrecognized command line token as the executable).Node: bioannExecutable: ABYSS-P--------------------------------------------------------------------------16 total processes failed to start/usr/bin/abyss-pe:503: recipe for target 'test-1.fa' failedmake: *** [test-1.fa] Error 134"Can you kindly help me to fix this errorThanks in advanceBest regardsAdlyAdly Abd-Alla (Ph.D.)
Professor of Entomology
Molecular Biologist
Insect Pest Control Laboratory (IPCL)
FAO/IAEA Agriculture and Biotechnology Laboratory
International Atomic Energy Agency, Vienna Austria
Tel: +431260028425, Fax: +4312600447
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