bcgsc/RNA-Bloom

is the assembly deterministic?

Closed this issue · 3 comments

alexyfyf commented

Please report

  • [ RNA-Bloom v2.0.1] version of RNA-Bloom with java -jar RNA-Bloom.jar -version
  • [ openjdk 11.0.13 2021-10-19] version of java with java -version
  • [ rnabloom -long ${raw_reads} -stranded -t 48 -outdir ${base}] exact command used to run RNA-Bloom

Hi,
I noticed the RNAbloom2 output for long read is non-deterministic and if I rerun with the same data, the result is slightly different (at least the number is not same). I'm wondering if this is designed or expected?

Thank you

kmnip commented

The assembly is not 100% deterministic, especially when multi-threading is used.

alexyfyf commented

The assembly is not 100% deterministic, especially when multi-threading is used.

Thank you for confirming this. So would it be deterministic in single thread? Just out of curiosity.

kmnip commented

The assembly is not 100% deterministic, especially when multi-threading is used.

Thank you for confirming this. So would it be deterministic in single thread? Just out of curiosity.

It should be deterministic in single thread.

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