IgPhyML lineage tree analysis does not work with test data

[Tommaso Andreani]

Hello,

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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:

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

But I have this error:

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START> BuildTrees
FILE> example.tsv
COLLAPSE> True

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?

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Thank you in advance for any feedback.

[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.

[Tommaso Andreani]

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..

[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

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[Tommaso Andreani]

I will check tomorrow and let you know thanks.

[Tommaso Andreani]

Hello,

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.

[Kenneth Hoehn]

Cool - I’ll mark this as resolved then.

[Kenneth Hoehn]

Was using older version of BuildTrees with new AIRR-formatted test data.