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
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--- Begin Message ---
Dear Sir/MsI recently installed Abyss assembler through the command
sudo apt-get install abysson 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 command line
parameter option (remember that mpirun interprets the first unrecognized
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 regardsAdly
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bcgsc/abyss
:microscope: Assemble large genomes using short reads - bcgsc/abyss
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Adly 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
--- End Message ---
