liftover failed with cross map about nf-lo

[RenzoTale88]

Hi Thanks for using nf-LO! Just paste the error log at the end please. Thanks Andrea

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________________________________ From: udiland ***@***.***> Sent: Wednesday, May 17, 2023 7:40:47 AM To: evotools/nf-LO ***@***.***> Cc: Subscribed ***@***.***> Subject: [evotools/nf-LO] liftover failed with cross map (Issue #13) Hi, I have a failure in running the pipline, couldnt understand exactly why. Maybe it is looking for chain.null file? Appreciate your help. Thank you! Here is the nextflow.log file (was to long to paste): https://tauex-my.sharepoint.com/:u:/g/personal/udiland_tauex_tau_ac_il/EVrh6dGhb4BOieTEvjfMbo0BcKncSEU42bVw8KarMUbEHg?e=yKs6Nu — Reply to this email directly, view it on GitHub<#13>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AFRTPKG3GZUZ2NF4OLVR53DXGRXG7ANCNFSM6AAAAAAYETZ6DA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[udiland]

Hello Andrea,
Thank you for your help.
Its looks like it fails in the crossmap stage.
Where can I find the error log you mention?
I see that the liftoff command looks not ok
This is what in the .command.sh file:
CrossMap.py null liftover.chain long_chrUn_filtered.vcf liftover.null
Thanks
Udi

[RenzoTale88]

Hi Udi, Try specifying `--annotation_format vcf` and see if that works. Andrea From: ***@***.***> Sent: 18 May 2023 19:02 To: ***@***.***> Cc: Andrea ***@***.***>; ***@***.***> Subject: Re: [evotools/nf-LO] liftover failed with cross map (Issue #13) Hello Andrea, Thank you for your help. Its looks like it fails in the crossmap stage. Where can I find the error log you mention? I see that the liftoff command looks not ok This is what in the .command.sh file: CrossMap.py null liftover.chain long_chrUn_filtered.vcf liftover.null Thanks Udi — Reply to this email directly, view it on GitHub<#13 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AFRTPKBJQDONQOBZT5LOJ2DXGZP4BANCNFSM6AAAAAAYETZ6DA>. You are receiving this because you commented.Message ID: ***@***.***>

[udiland]

Hi Andrea,

Thank you, it fix that issue, however I am getting another error.
The error is:
CrossMap.py: error: no such option: -a
When I look at the command it looks like this:
CrossMap.py vcf -a liftover.chain long_chrUn_filtered.vcf 190708.fasta liftover.vcf
I was able to produce the liftover vcf file by running the command without the -a option.

[RenzoTale88]

@udiland apologies for the late reply. This is a bug indeed. I'll work on a patch in the next days.

[RenzoTale88]

@udiland can you try the code now?
Be sure to clone the latest version:

git clone https://github.com/evotools/nf-LO
nextflow run ./nf-LO/ ...

Andrea

[udiland]

Hi Andrea,

I currently don't have the resources to run the analysis (I need to wait for others to finish their work).
I hope I will be able to check it soon.
Thank you for all the help.

Udi