error: TypeError: 'NoneType' object is not subscriptable

[huiluocao]

command line: python bigscape.py -i bgc_contigs_all_10k -o bgc_contigs_all_10k_bigscape_mix --mix

error msg: generate_network took 57.462 seconds Writing output files Calling Gene Cluster Families Cutoff: 0.3 Traceback (most recent call last): File "bigscape.py", line 3042, in clanCutoff=options.clan_cutoff, htmlFolder=network_htmlfolder) File "bigscape.py", line 1459, in clusterJsonBatch labels[bgcExt2Int[bgcSub2Ext[i]]] = bgcExt2Int[bgcSub2Ext_[exemplarsSub[labelsSub[i]]]] TypeError: 'NoneType' object is not subscriptable

[huiluocao]

can help figure out what happened?

[jorgecnavarrom]

What version of scikit-learn are you using (activate the BiG-SCAPE conda environment and do conda list | grep scikit)? Versions newer than v0.19.2 can sometimes cause errors in the clustering part.

[huiluocao]

I used v0.19.2. For some dataset, i run successfully, but not for this dataset. I can't find the difference between a failed one and a successful one.

On Wed, Jun 7, 2023 at 11:22 PM Jorge Navarro @.***> wrote:

What version of scikit-learn are you using (activate the BiG-SCAPE conda environment and do conda list | grep scikit)? Versions newer than v0.19.2 can sometimes cause errors in the clustering part.

— Reply to this email directly, view it on GitHub https://github.com/medema-group/BiG-SCAPE/issues/43#issuecomment-1581052215, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF4ACLYN54OZFARLZQ3GODLXKCME3ANCNFSM6AAAAAAY564RR4 . You are receiving this because you authored the thread.Message ID: @.***>

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[jorgecnavarrom]

Could you try to re-run but point to a different output folder (i.e. do not re-use the current output folder)? Another idea: if you are not using the clan mode, turn it off with --clans-off

[adraismawur]

Hi! We are closing issues after a while of inactivity. Please don't hesitate to re-open this issue if necessary!