Issue with Generating Layout File in Chopper and Inputting into Raptor Build Index

[Mercury0533]

Hi, i met some problems when i using it to build index

Here are the details of the issue:

Problem Description: I successfully generated a layout file using Chopper with the following command: chopper --input test.txt --kmer 32 --output test.layout however，when i try to put it into raptor to build an index: raptor build --input test.layout --output res.index and it shows erminate called after throwing an instance of 'std::filesystem::__cxx11::filesystem_error' what(): filesystem error: cannot get file size: No such file or directory [@CHOPPER_USER_BINS] /gpfs/biosoft/app2/miniconda3/envs/raptor/bin/raptor: line 31: 24047 Aborted (core dumped) raptor_avx2 "$@" i don't know whether i am using it correctly, and the version of Raptor is the latest 3.0.1

Another problem is about the document for usage in your github, it seems to return a 404 error

[eseiler]

Hey there,

the documentation links should work again.

As for the error, try using raptor layout instead of chopper. raptor layout is basically the compatible chopper version shipped with raptor. If you are using a standalone chopper installation, you'd need to use chopper 0.1.0.