Open mkillean opened 5 years ago
martinghunt
commented
5 years ago I can't think of anything obvious. Don't really get why it's saying it found /circlator/build/MUMmer3.23/nucmer but it thinks the version is < 3.1.
Maybe running progcheck with the --debug flag might help?
jgarbe256
commented
5 years ago __ checking nucmer ____ nucmer - not using environment variable nucmer - checking which(nucmer) ... got: "/opt/circlator/build/MUMmer3.23/nucmer" nucmer - checking version ... Running this command to get version: nucmer --version __ (begin output from nucmer --version)___ perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "C.UTF-8", LC_TERMINAL = "iTerm2", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). nucmer NUCmer (NUCleotide MUMmer) version 3.1
__ (end of output from nucmer --version)___ Looking far a match to the regex "([0-9.]+)" in the above output Match to this line: perl: warning: Setting locale failed. Got version: . Version of nucmer too low. I found ., but must be at least 3.1. Found here: /opt/circlator/build/MUMmer3.23/nucmer
kimnegrette3
commented
4 years ago Hi! did you manage to solve this? I am having the exact same output from circlator progchekc --debug. I have nucmer 3.1 but the version not being recognized. Any help would be really appreciated. Thanks!
jgarbe256
commented
4 years ago I wasn't able to get past this error, so I tried running circulator using the docker container instead.
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Hi! did you manage to solve this? I am having the exact same output from circlator progchekc --debug. I have nucmer 3.1 but the version not being recognized. Any help would be really appreciated. Thanks!
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mkillean
commented
4 years ago I was not able to get past the error either, and ended up converting the docker container to a singularity image.
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I wasn't able to get past this error, so I tried running circulator using the docker container instead.
On Wed, Aug 26, 2020 at 11:27 AM kimnegrette3 notifications@github.com<mailto:notifications@github.com> wrote:
Hi! did you manage to solve this? I am having the exact same output from circlator progchekc --debug. I have nucmer 3.1 but the version not being recognized. Any help would be really appreciated. Thanks!
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sanger-pathogens/circlator/issues/143#issuecomment-680986100, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEOV6A2ICX2GE3K5EDSLADDSCUZVNANCNFSM4GFP44WA .
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John Garbe, Ph.D. Informatics Lead | University of Minnesota Genomics Center | genomics.umn.eduhttp://genomics.umn.edu University of Minnesota | umn.edujgarbe@umn.edumailto:umn.edujgarbe@umn.edu | 612-807-3379
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kimnegrette3
commented
4 years ago Thank you! That totally solved the nucmer problem! But now I got some error with canu and java, did you happen to have something like this? ERROR: mhap overlapper requires java version at least 1.8.0; you have unknown (from 'java'). ERROR: 'java -showversion' reports:
I think the circlator team is not giving support right now, but I reaaaally need to use the program, so any little help you can give me I will appreciate a lot!!!
Thanks in advance!
Hi,
I am trying to install circlator on our HPC cluster. I am trying to use Singularity and convert the docker image, but I ran into an issue that I have been able to reproduce with the docker image directly, or a regular installation of circlator (and dependencies).
I have also been able to narrow this down to an issue with my environment variables, but I cannot locate which. To demonstrate this I will use my circulator 1.5.5 singularity image. Here is the error I receive in a normal environment:
However, the same command while stripping environment variables:
My question is if there is any way to determine which environment variable is causing this without having to go through each one independently? Our system uses lmod and we may run into issues using multiple modules and having their environment stripped.
Thanks for any help, Mike