Error in x$.self$finalize() about sierra

[rj-patrick]

Hi @AidenSb,

I believe the issue causing this error has been identified and fixed. Let me know if you continue to have troubles with the latest version of Sierra.

Cheers,
Ralph

[AidenSb]

Actually, I think this error is not causing my run to be halted.
would you please let me know what you think about this?

Error in { : task 1 failed - "1 elements in value to replace 0 elements"
Calls: CountPeaks -> %dopar% -> <Anonymous>
In addition: Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
3: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
4: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
5: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
Execution halted

[rj-patrick]

Hi @AidenSb,

It's not immediately clear what is causing this error. Can I clarify, are you able to run the Vignette example without error? And could you please give some more information on your inputs - what parameters you are setting in CountPeaks and the type of files you are working with? E.g. are you working with a 10x BAM file and what kind of GTF file you are using?

Cheers,
Ralph

[AidenSb]

Thanks Ralph, I will check it out again soon.

[pratarora]

I am facing the same error. I am using version 0.99.26. It doesn't seem to affect any downstream analysis though.

[borshago]

I get the same error for chrY, when processing 10x Chromium scRNA-seq data from female mice. I think it has to do with a lack of data for a particular chromosome. The error doesn't seem to cause any downstream issues.