cnvpytor run problem

Question

[hamideh]

hello I try to run cnvpytor with the command:

. cnvpytor -root file.pytor -rd 478m.sorted.bam -T genome.fa

But it stops length 1034 for all bmfiles and I get empty file

2024-10-14 08:31:08,786 - cnvpytor.root - INFO - Reading data for chromosome NKLS02001987.1 with length 1034
was killed

thanks for answer

Answer 1

[yura.grabovska]

Where are you running this analysis? Do you have sufficient memory to run the analysis. You might be running out of resources. Are you running this on a HPC?

[hamideh]

thanks for your answer. I use from server

[yura.grabovska]

I would definitely check if you're either running out of resources or if the server has specific rules for how jobs should be ran eg - queues if you're using a scheduler.