An error is detected in bootstrap fitting process

[zxwang-cloak]

Hi,

I got a quitting program when I performed the "sigflow bt" to run bootstrap signature fitting analysis in my own data. The error message was: "Cannot create 128 parallel PSOCK nodes. Each node needs one connection, but there are only 124 connections left out of the maximum 128 available on this R installation". So, how do I solve this problem with my existing server?

Best, zxwang

[ShixiangWang]

Could you provide more details about your commands and the operating system running the sigflow? Could you rerun it with less number of threads?

Have you achieved successful tests in https://github.com/ShixiangWang/sigflow/blob/master/test/test.sh or https://github.com/ShixiangWang/sigflow/blob/master/test/test_docker.sh?

[zxwang-cloak]

Thank you for your reply! My command is: sigflow.R bt -i input.maf -o ./bt-output -m MAF -h hg38 The operating system is: CentOS Linux release 7.9.2009 (Core) I tried to add "-T" to limit the cores, but it did not work. I had run successfully in "extract" and "fit" module.

[ShixiangWang]

@zxwang-cloak Thanks for your message. I checked the code and found that at default, all CPU cores are used for bootstrap fitting. I have updated https://github.com/ShixiangWang/sigflow and could you try using the latest code and re-run your data again?

[zxwang-cloak]

Thanks! I had updated the latest code, and I got a new error message:

""" Running signature bootstrap fitting pipeline...

[1] "hello0" An error is detected in bootstrap fitting process. Quit the program! object 'cores' not found """

My command is: sigflow.R bt -i input.maf -o ./bt-output -m MAF -h hg38 I also added the -T or --cores to limit the cores we used, but it did not cover the function in bt module.

[ShixiangWang]

Sorry, I did not test the code. I just tested it locally and updated it, please try again.

[zxwang-cloak]

It can now run successfully, thank you very much!

[ShixiangWang]

Good to hear that.