schraderL

Hi, I get the same error when trying to install via conda. Could you update the conda package, so it works with the new server address? Best lukas edit: I...

A quick addition: I can run `kallisto index` and `kallisto quant` just fine manually, when adding the `--make-unique` option to the indexing: ``` kallisto index -i CARD-0001/update_misc/getBestModel/bestModel CARD-0001/update_misc/getBestModel/transcripts.fa --make-unique kallisto...

Hi! I get the exact same error. Has this ever been resolved? Best Lukas

Hi @oushujun, check your email! cheers Lukas

Hi again, I now encountered the same problem again that dentist does not fill gaps (i.e. reduce the number of `N`s) in a scaffold assembly. This time, I scaffolded my...

Hi @a-ludi, here are the files. Thank you for looking into this! [collect.log](https://github.com/a-ludi/dentist/files/8999007/collect.log) [process.0.log](https://github.com/a-ludi/dentist/files/8999008/process.0.log) [process.1.log](https://github.com/a-ludi/dentist/files/8999009/process.1.log) [process.2.log](https://github.com/a-ludi/dentist/files/8999010/process.2.log) [process.3.log](https://github.com/a-ludi/dentist/files/8999011/process.3.log) [purged-output.log](https://github.com/a-ludi/dentist/files/8999012/purged-output.log) -lukas

Hi @a-ludi, will do! Can you say something why `dentist` did not reduce more of the `N`s in the assembly?

Hi @a-ludi, here are the `pile-ups*.db` files for that run. [pile-ups.zip](https://github.com/a-ludi/dentist/files/9030123/pile-ups.zip) cheers lukas