Nextclade ERR: The application panicked (crashed). about nextclade HOT 2 CLOSED

@Wen1953 If I understand correctly, you have created your own dataset, including, for example, files like genemap.gff and reference.fasta.

It seems that Nextclade tries to access the array gap_open_close here on line 23:

at index 1709, but it's length is less than that.

The gap_open_close is created on line 9, such that its length is equal to the length of reference sequence + 2, i.e. the length of sequence in reference.fasta, plus 2:

The array access on line 23 is happening on gene boundaries, as described by the genemap.gff.

My current hypothesis is that genes in your gene map go beyond the reference sequence length. This causes out-of-bounds array access, which causes the crash. Please make sure that your gene map correctly describes the reference sequence, and all genes fit inside its range.

It can also be an off-by-one bug in Nextclade. But I am currently not convinced that it's the case.

If in doubt, please upload your full dataset (e.g. to a GitHub repo) so that we can investigate.

So far Nextclade datasets have been mostly created by the Nextclade team, and we try to ensure that the different files within a dataset are compatible with each other. However, software should never panic and crash and also because there is an increase of interest by the community in creating new datasets, we should definitely add some error handling in this part of the code and to produce a more meaningful error message. If you have time and forces, feel free to contribute an improvement. This would help other people creating Nextclade datasets.

from nextclade.

Thanks @ivan-aksamentov . Your hypothesis was right, it was a problem with the files and the reference sequence length and not a nexclade bug. We are trying to work with some avian flu sequence even though there is not a database in nextclade. We are convinced that contribute with more databases to other pathogens will be very useful to science comunity.

from nextclade.