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NBISweden / IgDiscover-legacy

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads
https://www.igdiscover.se
MIT License
17 stars 10 forks source link

Error: No V genes were discovered in this iteration #103

Closed LandiMi2 closed 4 years ago

LandiMi2 commented 5 years ago

Hi I am getting this kind of error even if I run two iterations for my data set. I have confirmed the database V,D and J sequences match my sequences. What could be the problem, I am sure my data set should have new alleles present.

LandiMi2 commented 5 years ago

@marcelm please help.

marcelm commented 5 years ago

Can you tell me a bit more about the data? How many reads do you have? Which read lengths? From which sequencer?

marcelm commented 5 years ago

It may also be helpful if you could show the contents of the stats/stats.json file that was created by IgDiscover in the analysis directory.

Edit: Sorry, that file probably doesn’t exist if you get the error message you mention. Instead, any .json file in the stats/ directory would be interesting to see.

LandiMi2 commented 5 years ago

{ "version": "0.8.0", "reads": { "total": 285306, "merged": 272344, "merging_was_done": true, "trimmed": 272344 }, "iterations": [ { "size": 27 }, { "size": 0, "gained": 0, "lost": 27, "size_pre": 0, "gained_pre": 0, "lost_pre": 27 } ] }

LandiMi2 commented 5 years ago

actually the stat folder was generated , maybe I can share via email the details

LandiMi2 commented 5 years ago

Miseq sequencing platform was used

LandiMi2 commented 5 years ago

kindly share your email address please @marcelm

marcelm commented 5 years ago

I see that you’re using IgDiscover 0.8, which is very old. Many bugs have been fixed since then. Can you upgrade?

You can send e-mails to marcel.martin@scilifelab.se .

LandiMi2 commented 5 years ago

what is the new version ? is this how I upgrade? $conda install igdiscover=(version)

LandiMi2 commented 5 years ago

0.11-0 ?

marcelm commented 5 years ago

0.11 sounds good! conda update igdiscover should work, but also conda install igdiscover=0.11.