Issue: sample size of more than 100000 sequences about igor

[qmarcou]

Hello @kgrigaityte ,
For now IGoR is loading all alignments in memory and store them there, I guess this strategy problematic upon running over large alignment files. You should have a second line in the error message giving you the error type. Could you please paste the complete error message (or just edit your post with the complete error message) ?
There is a tradeoff between having to browse a large alignment file for every sequence on the fly (use virtually no memory but imposes to parse the complete file for each sequence) and storing every alignment in memory (uses a lot of memory and only parse the alignment file once).
In order to reduce memory usage there are two paths you could exploit:

• have a more drastic filtering on alignments upon aligning or reading alignments, by playing with alignment score thresholds or relative score thresholds (although now that I think about it I am not sure I have created a command line option for the latter yet).
• try and shorten your gene names (if you're using the IMGT complete name, the string will take up a lot of memory compared to a shorter name). This may sound silly but may be a real problem for large sequence sets.
  I'm a bit busy at the moment but I'll try and spend some time find a better tradeoff in terms of input reading for large dataset once I get some time
  Hope this helps!