Error in x$.self$finalize()

[AidenSb]

Hi Ralph, Thanks for this awesome tool. Can you please help me with this Error that happens in CountPeaks? >> "Error in x$.self$finalize() : attempt to apply non-function "

``

There are 3028 whitelist barcodes.
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
There are 118455  sites
Doing counting for each site...
Processing chr: chrX
 and strand 1
Processing chr: chr20
 and strand 1
Processing chr: chr1
 and strand 1
Processing chr: chr6
 and strand 1
Processing chr: chr3
 and strand 1
Processing chr: chr7
 and strand 1
Processing chr: chr12
 and strand 1
Processing chr: chr11
 and strand 1
Processing chr: chr4
 and strand 1
Processing chr: chr17
 and strand 1
Processing chr: chr2
 and strand 1
Processing chr: chr16
 and strand 1
Processing chr: chr8
 and strand 1
Processing chr: chr19
 and strand 1
Processing chr: chr9
 and strand 1
Processing chr: chr13
 and strand 1
Processing chr: chr14
 and strand 1
Processing chr: chr5
 and strand 1
Processing chr: chr22
 and strand 1
Processing chr: chr10
 and strand 1
Processing chr: chrY
 and strand 1
Processing chr: chr18
 and strand 1
Processing chr: chr15
 and strand 1
Processing chr: chr21
and strand 1
Processing chr: chrM
 and strand 1
Processing chr: KI270713.1
 and strand 1
 and strand -1
Processing chr: KI270711.1
 and strand 1
 and strand -1
Processing chr: GL000205.2
 and strand 1
 and strand -1
Processing chr: KI270728.1
 and strand 1
 and strand -1
Processing chr: GL000219.1
 and strand 1
 and strand -1
Processing chr: KI270727.1
 and strand 1
 and strand -1
Processing chr: GL000194.1
 and strand 1
 and strand -1
**Error in x$.self$finalize() : attempt to apply non-function**
In addition: Warning message:
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.

``

Cheers,

[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

[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]

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.