circlator
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sanger-pathogens
Version of numcer too low (v1.5.5)
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:
singularity exec circlator-1.5.5.img circlator progcheck
Circlator version: 1.5.5
External dependencies:
bwa 0.7.12 /circlator/build/bwa-0.7.12/bwa
canu 1.4 /circlator/build/canu-1.4/Linux-amd64/bin/canu
Version of nucmer too low. I found ., but must be at least 3.1. Found here:
/circlator/build/MUMmer3.23/nucmer
prodigal 2.6.2 /circlator/build/prodigal-2.6.2/prodigal
samtools 1.3 /circlator/build/samtools-1.3/samtools
spades 3.7.1 /circlator/build/SPAdes-3.7.1-Linux/bin/spades.py
Python version:
3.6.7 (default, Oct 21 2018, 08:08:16)
[GCC 8.2.0]
Python dependencies:
openpyxl 2.5.10 /usr/local/lib/python3.6/dist-packages/openpyxl-2.5.10-py3.6.egg/openpyxl/__init__.py
pyfastaq 3.17.0 /usr/local/lib/python3.6/dist-packages/pyfastaq-3.17.0-py3.6.egg/pyfastaq/__init__.py
pymummer 0.10.3 /usr/local/lib/python3.6/dist-packages/pymummer-0.10.3-py3.6.egg/pymummer/__init__.py
pysam 0.15.1 /usr/local/lib/python3.6/dist-packages/pysam-0.15.1-py3.6-linux-x86_64.egg/pysam/__init__.py
However, the same command while stripping environment variables:
[]$ singularity exec --cleanenv circlator-1.5.5.img circlator progcheck
Circlator version: 1.5.5
External dependencies:
bwa 0.7.12 /circlator/build/bwa-0.7.12/bwa
canu 1.4 /circlator/build/canu-1.4/Linux-amd64/bin/canu
nucmer 3.1 /circlator/build/MUMmer3.23/nucmer
prodigal 2.6.2 /circlator/build/prodigal-2.6.2/prodigal
samtools 1.3 /circlator/build/samtools-1.3/samtools
spades 3.7.1 /circlator/build/SPAdes-3.7.1-Linux/bin/spades.py
Python version:
3.6.7 (default, Oct 21 2018, 08:08:16)
[GCC 8.2.0]
Python dependencies:
openpyxl 2.5.10 /usr/local/lib/python3.6/dist-packages/openpyxl-2.5.10-py3.6.egg/openpyxl/__init__.py
pyfastaq 3.17.0 /usr/local/lib/python3.6/dist-packages/pyfastaq-3.17.0-py3.6.egg/pyfastaq/__init__.py
pymummer 0.10.3 /usr/local/lib/python3.6/dist-packages/pymummer-0.10.3-py3.6.egg/pymummer/__init__.py
pysam 0.15.1 /usr/local/lib/python3.6/dist-packages/pysam-0.15.1-py3.6-linux-x86_64.egg/pysam/__init__.py
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
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?
__________ 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
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!
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 [email protected] 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!
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I was not able to get past the error either, and ended up converting the docker container to a singularity image.
On Aug 26, 2020, at 10:47 AM, jgarbe256 <[email protected]mailto:[email protected]> wrote:
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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 <[email protected]mailto:[email protected]> 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 | [email protected]mailto:[email protected] | 612-807-3379
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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!