transrate error about salmon version

Question

[yinbinqiu]

hi, all When using software transrate to analyze the quality of the transcript assembled from scratch, the command used is

**transrate --assembly xxx.fa --left left_fq.gz --right right_fq.gz --output ./**

Found that the salmon version reported an error, Initially the following error occurred

Dependencies are missing: - salmon (0.6.0) You are running the packaged version of transrate This comes with the read-metrics dependencies pre-installed

Then, I installed the latest version of salmon v1.1.0, ran the command again, and found an error.

*[ERROR] 2020-02-28 13:33:51: Version Info: ### A newer version of Salmon is available.
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains ** important bug fixes ** and improvements; please upgrade at your
earliest convenience.
[ERROR] 2020-02-28 13:33:51: Salmon failed*

How can I solve this problem? Very much looking forward to an effective solution.

Answer 1

[ATpoint]

There is quite a jump from v0.6.0 to v1.1.0. Since v.1.0.0 the indexing structure has changed, see the release notes: https://github.com/COMBINE-lab/salmon/releases

Therefore you will need to re-index your transcriptome. I guess that is the main issue here.