Feng Yu

it seems like I didn't save that folder, anyway I ran it with canu as the assembler and it went well without any error. I checked the spade log file...

[variant_manip.cpp:75 is_ref_consistent] Variant is not consistent: SCKP140071_chr:355431-355441 - GAAAAAAAGTC(REF) vs GATCCTGCTGG(FASTA) [normalize.cpp:178 normalize] Normalization not performed due to inconsistent reference sequences. (use -n option to relax this) Pretty much the...

Hi @VadimDu After some tests, the error seems to arise from the recent update (2015.11.10-h5ef6573_4) of dependency vt. I solved the problem by rolling vt back to version 2015.11.10-he941832_3.

I replicated your result with your test data on Snippy 4.6.0, and any idea to fix this? Thanks

@fredyr could please share your work-around as I suppose this bug would greatly affect the downstream recombination filtering step, which relies on gap characters, such as Gubbins. Many thanks

any update regarding this issue?

about masking phage using predictions from PHASTER, should I mask the intact phage only or mask all phage regions detected by PHASTER even they are not intact (e.g. regions only...

I'm using Krakenuniq with the pre-built database downloaded from https://benlangmead.github.io/aws-indexes/k2, the 384G one labelled as EuPathDB48, to generate the report file. Bracken was installed by the install shell rather than...

I've got the same issue. Anyone wanna share a solution? Many thanks. I'm using Krakenuniq with the pre-built database downloaded from https://benlangmead.github.io/aws-indexes/k2, the 384G one EuPathDB48, to generate the report...