X nodes produced errors; first error: missing value where TRUE/FALSE needed

[anfarr]

Hello Simon,
first thank you for providing your program on github.
I am currently trying to use your tool in a nextflow pipeline. So far the first function works as intended.
However i had some problems with your second function "APERO_end_detection".

When using it with a ptt file, i realized that in line 509 the variable ptt had to be refactored to ptt_file

- fii = annot_apply_RNA_ptt(f, ptt, genome_size)
+ fii = annot_apply_RNA_ptt(f, ptt_file, genome_size)

My first tests were successful in creating an output of the second function by simply running it in a singularity container on our cluster. Calls for APERO_end_detection were distributed via slurm to one node each with four threads respectively.
However, when i do the same with nextflow and let it handle the slurm scheduling the majority of return values being generated by the APERO_end_detection calls are "NA".

The corresponding errors are:
X nodes produced errors; first error: missing value where TRUE/FALSE needed
where X is 1 < X <= "chosen number of threads".

Maybe it is related to this problem https://stackoverflow.com/questions/16895848/results-of-workers-not-returned-properly-snow-debug. Although i am not sure why this is only the case when nextflow handles the scheduling.

Maybe you have an idea.

[Simon-Leonard]

Hi,

Thank you for pointing out the code mistake.
Concerning the nextflow issue, I never tried to run APERO with nextflow and I don't have any idea about what is happening.
I suppose that you used the same APERO command with singularity and nextflow ?

Simon

[anfarr]

Hey,
i wrote a small parser for the two functions, that is being run in the singularity container. But in essence the parameters being passed to APERO were the same. I will double check. For now i wrote a bash script that schedules the slurm jobs (running APERO in the singularity container on my files).

Edit: closed on accident

Anton