Hi! I’m wondering if anyone else here has encountered this issue with linx and how they fixed it? https://github.com/nf-core/oncoanalyser/issues/257 Thanks in advance!

Hi @Eva Caceres, would you be able to send across the log file you mentioned?

Will do later today! Thanks a lot for taking the time and checking

The genome version seems to have fixed this issue it seems 🙂

Hi Rayan, as far as I know this issue is not fixed. For us, who are testing and want to be able to run genome version 37, this is still an issue and we would love some guidance

Hi Eva, no worries - can you share more details ? Logs, configs, commands, etc - then we can take a deeper look :)

I can share the logs with you too. Thank you!

Hi Eva, could you have a look at the svs in the linx logs and check if there's any data in the SAMPLE.purple.cnv.gene.tsv and/or SAMPLE.purple.cnv.somatic.tsv ? (and check if PURPLE ran smoothly) - this could rule out coverage issues

Thanks for picking this up again @Rayan Hassaïne - I haven’t been able get back to investigating the issue between the upcoming release work

purple completed without issues

is there any concordance between PURPLE and LINX output for a given SV? Perhaps trace it between the tools - Feel free to send me these files privately if need be

just for me to understand, should the

svID

from the linx error message match the

SVID

field in the purple vcf file? is that what you’re asking

could you share the entire linx logs? i.e. the .command.log file of that process

it has been generated. I’ll send it privately. Thanks