Rarefaction

[eduardags12]

I'm having a problem when I run rarefaction, it never finishes, it stays at 2679/2680.

[axbazin]

Hi,

Could you share the log of your analysis ?
And, if possible, the genomes and command line you used to reach this problem (if it is not possible it's perfectly understandable).

Adelme

[eduardags12]

Thank you very much for your feedback, I'll send you the code I used to generate the rarefaction, as well as a printout of what my screen looks like without finalizing it. Code: find $PWD/gff/ -name '*.gff' > gff_list_pangenome.ts cat gff_list_pangenome.tsv | parallel echo -e "{/.}'\t'{}" | sponge gff_list_pangenome.tsv conda activate ppanggolin ppanggolin workflow --anno gff_list_pangenome.tsv -o 11_ppanggolin --cpu $(nproc) -f ppanggolin info -p 11_ppanggolin/pangenome.h5 --content > 11_ppanggolin/content.txt ppanggolin info -p 11_ppanggolin/pangenome.h5 --parameters > 11_ppanggolin/parameters.txt ppanggolin rarefaction --cpu $(nproc) -p 11_ppanggolin/pangenome.h5 -o 11_ppanggolin/rarefaction Att, Eduarda Em seg., 18 de mar. de 2024 às 12:45, Adelme Bazin ***@***.***> escreveu:

…

Hi, Could you share the log of your analysis ? And, if possible, the genomes and command line you used to reach this problem (if it is not possible it's perfectly understandable). Adelme — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBCB63EPTQXWEOBYMMVWY3DYY4D25AVCNFSM6AAAAABE3VOV22VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBUGI3TGNRWGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Eduarda Guimarães Sousa * Mestranda em Genética: Genômica, Bioinformática Laboratory of Cellular and Molecular Genetics Institute of Biological Sciences Federal University of Minas Gerais (34) 996795082

[axbazin]

Hi,

Thank you for the command lines, they are used exaclty as expected, so nothing to change there and there is likely a bug for us to find. Would you mind sharing the log that was printed out when you ran those?

Adelme

[eduardags12]

Hi, Thank you for your feedback, but I can´t find the log that was printed out. Eduarda Em ter., 2 de abr. de 2024 às 12:10, Adelme Bazin ***@***.***> escreveu:

…

Hi, Thank you for the command lines, they are used exaclty as expected, so nothing to change there and there is likely a bug for us to find. Would you mind sharing the log that was printed out when you ran those? Adelme — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBCB63AEKKYBLFA57R5DDOLY3LC6ZAVCNFSM6AAAAABE3VOV22VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZSGMYTONZQGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Eduarda Guimarães Sousa * Mestranda em Genética: Genômica, Bioinformática Laboratory of Cellular and Molecular Genetics Institute of Biological Sciences Federal University of Minas Gerais (34) 996795082

[axbazin]

Hi,

I'm afraid I can't do much without more information, sorry.
I'm not sure I remember meeting a case where the rarefaction was hanging. I assume it can come from NEM, maybe @ggautreau you remember if there is an edge case where this step can hang ?

Adelme

[ggautreau]

Hi both of you,

This should not result in an endless computation. Could you share your dataset @eduardags12 to help replicate this issue?

Thx.

[eduardags12]

Sure, here it is. https://drive.google.com/drive/folders/1xpHpLHo2TbAgYGOriyQr9rPMnEijfp48?usp=drive_link Att, Eduarda Em sex., 5 de abr. de 2024 às 12:59, Guillaume GAUTREAU < ***@***.***> escreveu:

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Hi both of you, This should not result in an endless computation. Could you share your dataset @eduardags12 <https://github.com/eduardags12> to help replicate this issue? Thx. — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBCB63GZGL2AZUPPPRJLDR3Y33C4TAVCNFSM6AAAAABE3VOV22VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBQGE3DEMZTGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- *Eduarda Guimarães Sousa * Mestranda em Genética: Genômica, Bioinformática Laboratory of Cellular and Molecular Genetics Institute of Biological Sciences Federal University of Minas Gerais (34) 996795082

[jpjarnoux]

Hi @eduardags12
Sorry for the delay. What is the status of this issue?

[jpjarnoux]

Hi!

We were able to work on your data. We got stuck at the annotation stage because we couldn't manage the coordinates on several lines. This bug has been fixed in PR #240.

Having done this, I didn't have any problems with partitioning.

You can use the dev version of PPanGGOLiN, which includes this change. Here it's how to install it https://ppanggolin.readthedocs.io/en/latest/user/install.html#development-version

A release will be available soon for installation via conda.