microtrait hanging on sample data example

sheaster commented 2 years ago

Hi there, I've installed microtrait (and reinstalled it) on R 4.0 with and prodigal/2.6.3, hmmer/3.1b2

when trying to run the single genome example, the program hangs after run.hmmsearch has run.

This output after the following two commands is quoted below genome_file <- system.file("extdata/examples/2775507255/in/2775507255.fna", package="microtrait") microtrait_result = extracttraits(genome_file)

Running prodigal for 2775507255.fna run.prodigal: 9.471 sec elapsed Running hmmsearch for file128c673ed37 Running hmmsearch for file128c673ed37 run.hmmsearch: 124.921 sec elapsed

and then nothing.

I am fairly certain I installed microtrait and piggybacked the files correctly.

Can you please suggest what I may have done wrong?

Thanks, Shea

deanpettinga commented 2 years ago

I'm also really interesting in testing this software on my dataset, but I'm experiencing the same error in the tutorial dataset.

> genome_file <- system.file("extdata/examples/2775507255/in/2775507255.fna", package="microtrait")
> microtrait_result = extracttraits(genome_file)
Running prodigal for 2775507255.fna
run.prodigal: 15.744 sec elapsed
Running hmmsearch for file3106b53fdd7
Running hmmsearch for file3106b53fdd7
run.hmmsearch: 118.657 sec elapsed
Loading required namespace: testthat

I'd love to get this software working if possible. Please advise!

cheers, Dean

casett commented 2 years ago

I am also encountering this issue. @ukaraoz has a solution been found?

ukaraoz / microtrait

microtrait hanging on sample data example #2