Anton Korobeynikov

Your second spades.log clearly shows that the scaffolds.fasta are there and processed: ``` == Processing of scaffolds == Running contig polishing tool: /home/luke831215/tools/SPAdes-3.11.1-Linux/bin/corrector /home/ph/mnt/biocollab/GAGE-B/b-sides/R_sphaeroides_MiSeq/assembly/mismatch_corrector/scaffolds/configs/corrector.info /home/ph/mnt/biocollab/GAGE-B/b-sides/R_sphaeroides_MiSeq/assembly/misc/assembled_scaffolds.fasta == Dataset description file was...

> Sorry, this should be right. Doesn't seem so. The log has: ``` == Processing of scaffolds == Running contig polishing tool: /home/luke831215/tools/SPAdes-3.11.1-Linux/bin/corrector /home/ph/mnt/biocollab/GAGE-B/b-sides/R_sphaeroides_MiSeq/assembly/mismatch_corrector/scaffolds/configs/corrector.info /home/ph/mnt/biocollab/GAGE-B/b-sides/R_sphaeroides_MiSeq/assembly/misc/assembled_scaffolds.fasta == Dataset description file was...

25k HMMs? Wow, that's a lot. How long are the HMMs?

Hello Andreas, Thanks for letting us know! Does Debian ship the latest version of SPAdes? Last time I checked it still shipped 2.5 year old SPAdes 3.13

FWIW: our development server is running Debian and release packaging & testing is done there. We certainly do not see any troubles building and given that there were no user...

Hello No, nothing like this is planned. Will it be possible for you to describe your setup when trusted contigs are available / used?

``--trusted-contigs`` is certainly a fully supported option. The typical usage of it is follows: you're having and old assembly of the same sample, but you happen not to have these...

Steps to implement: * Build SPAdes using clang (and ninja) * Build SPAdes using additional `-H` flag * Parse build log using script from Chrome: https://source.chromium.org/chromium/chromium/src/+/HEAD:tools/clang/scripts/analyze_includes.py

will you please provide the full logs as an attachment?

Hello > I am not sure how to set the k parameter, yet. Suggestions are very welcome ! If you're unsure what to do – simply stick to the default....