"protein(s) without contig" leading to "ERROR:vcontact2: Error in contig clustering"
Hi,
I'm trying to run vcontact2 on two phage contigs, but I keep getting "protein(s) without contig" warnings in "Building the cluster and profiles" followed by a possibly related fatal error in "Contig Clustering & Affiliation" ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: 'DataFrame' object has no attribute 'ix'
A log of the run and my gene-to-genome mapping file are attached. I'm running vcontact2-0.9.13 installed via conda on an ubuntu 18.04 system.
Any help would be appreciated
Comments (11)
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And apparently that can be solved by downgrading pandas (https://bitbucket.org/MAVERICLab/vcontact2/issues/17/error-vcontact2-error-in-contig-clustering).
Sometime it just helps talking out loud . Sorry for the fuss.
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Ok, also had to downgrade to python=3.7 for panda=0.25.3 to work. But now I get another error…
------------------------Contig Clustering & Affiliation------------------------- Loaded graph with 2243 nodes and 79278 edges [====================] 100% Growing clusters from seeds... [====================] 100% Finding highly overlapping clusters... [====================] 100% Merging highly overlapping clusters... Detected 319 complexes ERROR:vcontact2: Error in viral clusters ERROR:vcontact2: type object 'object' has no attribute 'dtype'
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Have the same issue by running the test data set.
ERROR:vcontact2: Error in viral clusters
ERROR:vcontact2: type object 'object' has no attribute 'dtype'python=3.8.6 and pandas=0.25.3
Looking forward for help!
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What worked for me, in the end, was installing the right pandas and python first:
# python needs to be 3.7 for pandas < 1.0 conda create --name vContact2 python=3.7 # NOTE the explicit 3.7 python here conda activate vContact2 pandas need to be 0.25.3 - https://bitbucket.org/MAVERICLab/vcontact2/issues/17/error-vcontact2-error-in-contig-clustering conda install pandas=0.25.3 conda install vcontact2 conda install -y mcl blast diamond
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Thanks a lot @Thomas Hackl!!
I reinstalled using your order and package version. Now it is working!
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I’m having the same error with the example data. I tried specifying the versions of pandas (0.25.3) and python (3.7.9) like you suggested @Thomas Hackl , but I’m still getting the same error message. If anyone has any other suggestions, I’d greatly appreciate them. Thanks!
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In case someone is still having the “ERROR:vcontact2: Error in viral clusters, ERROR:vcontact2: type object 'object' has no attribute 'dtype'“ error, downgrading numpy to
numpy=1.19.5
seemed to work for me. I’m not sure if also specifying python=3.7 and pandas=0.25.3 is also needed with this fix though because I did do that as well and continued to have the same error before downgrading numpy. -
I updated both the Singularity definition file and setup.py requirements to enforce numpy and pandas versions, but I haven’t yet gotten to Anaconda, so if you installed vContact2 through Anaconda, a quick fix was posted by Thomas. Indeed, using pandas <=0.25.3 and numpy <1.19.5 should resolve this issue.
I will also add a check to ensure headers are enforced in the gene-to-genome file…
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thanks for the additional fixes! I appreciate the help greatly. Unfortunately, I have a new error that is identical to that in issue 36, so commented there with the new problem.
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- changed status to resolved
Closing this as it's due to absent headers or use of .ix. A check for headers will be included in 0.9.22. Pandas versioning will be used to avoid .ix depreciation.
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OK, red herring = the "protein(s) without contig" errors occur ed because I forgot the header line in the “gene-to-genome”.csv…
However, even with the proper mapping file I get: