Creating ARROWs

[karenpaiva]

I'm having problems creating the arrows.
I used the gff3 file from Phytozome to create gene annotation
geneAnnotation <- createGeneAnnotation( TSS = TSS, exons = exons, genes = genes )
This is my TSS before creating the GeneAnnotation:
GRanges object with 34681 ranges and 1 metadata column: seqnames ranges strand | gene_id <Rle> <IRanges> <Rle> | <character> Potri.001G000400.v4.1 Chr01 17702 - | Potri.001G000400.v4.1 Potri.001G000450.v4.1 Chr01 14997 - | Potri.001G000450.v4.1 Potri.001G000500.v4.1 Chr01 43197 - | Potri.001G000500.v4.1 Potri.001G000600.v4.1 Chr01 50630 + | Potri.001G000600.v4.1 Potri.001G000700.v4.1 Chr01 65133 - | Potri.001G000700.v4.1

And the genome annotation I used the fasta files to build the BSGenome object

But I keep getting this error:
2025-02-28 10:36:37.295905 : (scATCA_Populus : 1 of 1) Successful creation of Temporary File, 5.617 mins elapsed.
2025-02-28 10:36:37.297907 : (scATCA_Populus : 1 of 1) Creating ArrowFile From Temporary File, 5.617 mins elapsed.
2025-02-28 10:38:24.268829 : (scATCA_Populus : 1 of 1) Successful creation of Arrow File, 7.4 mins elapsed.
2025-02-28 10:38:33.537914 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-49f23206da22-Date-2025-02-28_Time-10-31-00.190801.log

This is my log file:

ArchR-createArrows-49f23206da22-Date-2025-02-28_Time-10-31-00.190801.log

How can I fix this error to proceed with the analyses.

[immanuelazn]

Hi @karenpaiva! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
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