File families.fa.strained is empty in the summaryFiles directory

[Zhenlisme]

Hello Toby,

Thank you for developing EarlGrey to improve TE annotation.

I am using the latest version of EarlGrey (v5.0.0) to annotate TEs for Xenopus genome (genome size ~ 2.7 Gbp). Below is the parameter I used: earlygrey -g Xenopus.fa -s Xenopus_laevis -o opt_dir -t 20 -e yes

The program ran smoothly and no error message was reported. And the Helitron annotation from HELIANO was successfully integrated into the gff file. But I found the file families.fa.strained under summaryFiles/ directory is empty and I did not find any TEs generated from RepeatModeler2 in the filteredRepeats.gff file (no TE name started with RND).

I am wondering if this is due to an bug of the latest version as one of my colleague has the same issue while using EarlGrey (v5.0.0)?

Thank you again for your time and help.

All the best, Zhen

[TobyBaril]

Hi Zhen!

Can you check which build you are using of v5.0.0? There were some issues with build 0, whilst build 1 tested and completed as expected. It took longer than expected for build 1 to release, so if you tried to install shortly after it was released, build 0 might have been used.

Thanks,

Toby

[Zhenlisme]

Hello Toby,

I checked the meta.yaml file and indeed it is build 0. Thank you for letting me know. I will reinstall the latest version with build 1.

By the way, could you please make it clear for the HELIANO version and parameters used in EarlGrey pipeline in case some users want to try different parameters?

Thanks a lot, Zhen

[TobyBaril]

Great! I am also re-testing to check everything is working as expected! I have added a note in the release note of the README section.

[Zhenlisme]

Thank you !