Anton Korobeynikov
Anton Korobeynikov
Sorry, spades.log is broken
Hello Thanks for the suggestions. First of all, SPAdes does not track which regions came from trusted contigs and, as in many de Bruijn-graph based assemblers the correspondence to the...
Thank you for your interest in SPAdes. This is known issue, we will try to fix it in SPAdes 3.12.1
The only "workaround" so far is to skip the read error correction step via --only-assembler. The results ought to be sub-optimal though and the assembly would require much more time...
It's likely the same issue. We hoped to get it fixed, but most probably some corner cases still remains.
@ammaraziz There is no problem in your case. Subclustering might be slow depending on your dataset. Though, there stuck could be caused by I/O problems on your end.
Hello This is known problem with CQF library we're using. For some reason it just stuck. We hope to be able to at least somehow workaround this issue in the...
@ralsallaq This is known problem with CQF implementation. So far there is no workaround. You may want to try --only-assembler after quality trimming
No work was done in 3.15 to address this issue due to lack of bandwidth. You may skip the read error correction, the running time and memory consumption might be...
The difference in assembly results are surely expected. Note that read error correction could certainly (falsely) collapse the variation as it might be hard to distinguish the sequencing artefacts from...