Could not create pipe to check startup of child (Too many open files)

a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.

https://a-ludi.github.io/dentist/

MIT License

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Could not create pipe to check startup of child (Too many open files) #31

Open lucabianco78 opened 2 years ago

lucabianco78 commented 2 years ago

Hi,

I am using ONT data and I got the error in the title from the pileupCollector (in the collect.log). I tried to increase the number of tolerated opened files with: ulimit -n 100000 and I set the batch_size: 100 in the snakemake.yml file but this did not solve the problem. Any advice on how to solve this?

Thanks a lot!

a-ludi commented 2 years ago

Hi,

I have heard about this problem from @diego-rt and tried to fix it without any luck so far. I will continue with debugging and report here.

Can you tell me how much input data you have?

lucabianco78 commented 2 years ago

Hi,

Thanks for your help! I have ~7.5 million ONT reads and the genome sequence has ~800Mbps split in 3000 sequences.