Error in the section of modelAndMaskGenome_wf:tidy_to_gff3

[sherlock0088]

Hi,

I got an error message when I run repeatmodeler2_nf. This error exist no matter I run with example data or my own data. Just wondering if you can fix it.

Best, Yupeng

[photocyte]

Hi there Yupeng. Interesting, thanks for sharing.

First off, I think you could probably just comment out the tidy_to_gff process & soft_mask process in the main.nf if you don't mind not having the GFF (pretty sure RepeatModeler doesn't make a GFF by default anyway) https://github.com/photocyte/repeatModeler2_nf/blob/cc5d7507a7fef0c724c317ff8791a31cfb613857/main.nf#L250 https://github.com/photocyte/repeatModeler2_nf/blob/cc5d7507a7fef0c724c317ff8791a31cfb613857/main.nf#L251

Could you send me line 60 and 61 of the file gt is complaining about? If you aren't familiar with Nextflow, you would have to navigate to the work/37/8f099a... (use tab completion) directory, and then rerun cat tmp.gff | grep -vP "^#" to create the file that gt was seeing.

[sherlock0088]

Hi,

Here I attach the complete gff file since the file is not large. tmp.gff.txt I guess gt was complaining about there are 2 lines with ID=60.

Yupeng

[photocyte]

Hi,

I'd have to guess that the issue might be my merging logic for mixing RepeatMasker_parallel_exec and RepeatMasker_simple_exec, gt merge would probably fix this http://genometools.org/tools/gt_merge.html , but the IDs would end up getting renamed which isn't necesarrily a benefit. But arguably having the RepeatMasker_simple_exec was premature optimization in the first place, and could be removed. If you'd like to make a pull request to address any of these solutions, happy to take a look!

[sherlock0088]

Hi, I don't think gt merge could really help. Will see other suggestions.

Yupeng