No partition in the output

[NikaAb]

Dear Duncan,

I have run partis on some of my fasta files, coming from CLL patients. In the output dictionary, the partition list is empty, I wonder if I use the right command.

This is how I run the partis :

(base) root@8788e7f742a7:/partis/bin# ./partis annotate --infname /host/home/patients/P5.fa --outfname /host/home/P5_partis.yaml --n-procs 8

This is what I get :

annotating smith-waterman vsearch: 161985 / 162742 v annotations (757 failed) with 41 v genes in 37.2 sec reading sw results from _output/_host_home_patients_P5/sw-cache-7901971560392386892.yaml info for 161983 / 162742 = 0.995 (759 failed, 80553 duplicates) kept 22836 (0.140) unproductive water time: 39.8 hmm prepare_for_hmm: (8.6 sec) running 8 procs calcd: vtb 81430 fwd 0 min-max time: 196.9 - 203.2 sec read output processed 81430 hmm output lines with 81407 sequences in 81407 events (23 failures) warning skipped 15 invalid events warning no valid paths: S157058 S45210 S73099 S82197 S82809 S107180 S109301 S68536 infra time: 91.8 hmm step time: 335.8 total time: 432.4

And this is what I have in the output dictionnary :

>>> partis_output.keys() dict_keys(['version-info', 'germline-info', 'events', 'partitions']) >>> partis_output['partitions'] []

I looked also into the events, all the sequences are not invalide, I can't see where is the probleme. Do you have any idea ? Thanks a lot ! Nika

[psathyrella]

Yes, you'll want to run partition to get clonal family clusters; annotate makes just annotations. See the descriptions here.

[NikaAb]

Great, thanks! That was the first thing to verify, and I missed it!