IgPhyML lineage tree analysis does not work with test data

Issue #85 resolved
Tommaso Andreani created an issue


I am trying to reproduce the example of IgPhyML lineage tree analysis that i found at this link here. For this i download the example data and run the command, as explained in the tutorial:

BuildTrees.py -d example.tsv --outname ex --log ex.log --collapse --sample 3000 --igphyml --clean all --nproc 1

But I have this error:

START> BuildTrees
FILE> example.tsv

PROGRESS> 08:48:41 |Correcting frames and indels of sequences | 0.0 minWARNING> FUNCTIONAL column not found.
ERROR> Cannot export datasets until sequences are clustered into clones.

Are you experiencing the same error if you try to reproduce it?

Thank you in advance for any feedback.

Comments (9)

  1. Kenneth Hoehn

    The example data works on my system. Are you using the latest version of Change-O (v1.0.0)? It seems likely that this is caused by BuildTrees expecting a Change-O formatted table as input rather than AIRR tsv format. We switched everything (including the example data) over to AIRR tsv recently.

  2. Tommaso Andreani reporter

    I have installed immcantation with the last docker image. Does it have Change-O v1.0.0? I do not have my workstation with me at the moment..

  3. Kenneth Hoehn

    Seems to work with the Immcantation 4.0.0 Docker image on my system. Worth checking the version numbers on your workstation when you can. You can do this with:

    BuildTrees.py --version

  4. Tommaso Andreani reporter


    I checked the version and for the error you see above i was using my local machine in whích BuildTrees.py was initially installed long time ago with pip. (my mistake sorry, i wrote above that i was using the docker). The version of BuildTrees.py in my local machine is 0.4.4-2018:

    BuildTrees.py --version
    BuildTrees.py: 0.4.4-2018.10.27

    I then moved to the docker installation (the last version 4.40) that I have in the cloud in which the version for BuildTrees.py is:

    BuildTrees.py --version
    BuildTrees.py: 1.0.0 2020.05.06

    and the changeo is changeo-1.0.0-py3.7.egg-info

    here it works perfectly.

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