Robert Vaser
Robert Vaser
Hello Valentine, looking at the log I suspect that minimap crashed due to insufficient memory. How much RAM do you have? How large are your reads? Best regards, Robert
Hmmm, not sure what minimap requirement is, but it seems to me that 120GB should be enough.
Hi Julien, please run the following commands from ra root folder and paste the output here: ```bash cd vendor/rala git status git log ``` Best regards, Robert
Please run `head -n 1016410 zander_pooled.subreads.renamed.fasta | tail -n 2` and paste the sequence causing the problem here.
Please also run `git log` from ra/vendor/rala.
As each sequence is usually represented with two lines in FASTA format (one for header and one for the data), we are using `2 * read_id + 2` to obtain...
Wrapped files are forking for me. Do you mind sending me your file so I can investigate further?
I understand, that is a lot of data. The error occurred in the layout step where only TGS data is used. Can you please provide me with the command you...
That looks fine. I am not sure what could be wrong. By the extension .renamed.fasta, did you perhaps rename your reads with ids? If so can you `grep` the reported...
Can you please replace this lines https://github.com/rvaser/rala/blob/iterative/src/overlap.cpp#L55-L57 (located at `vendor/rala/src/overlap.cpp`) with: ```cpp fprintf(stderr, "[rala::Overlap::transmute] error: " "unequal lengths in sequence and overlap file for sequence with id %lu (%u -...