BiocParallel error when putting multiple .bam files as inputs for reads

[TingQi2020]

Dear Bambu Team,

I'm putting multiple .bam files as inputs for reads, but I'm getting an error. Please find the attached log file.

This is my code: bambuAnnotations <- prepareAnnotations(gtf.file) file_list = list.files(path = bam_dirt, pattern = "genome\.sort\.bam$", full.names = TRUE) se.multiSample <- bambu(reads = file_list, annotations = bambuAnnotations, genome = fa.file,opt.discovery = list(min.txScore.singleExon = 0),ncore=ncore,verbose=TRUE,lowMemory=TRUE)

Thank you in advance.

bambu_multiSample_error.txt

[andredsim]

Hi,

This looks very similar to another issue. See this comment for some troubleshooting/workarounds. https://github.com/GoekeLab/bambu/issues/411#issuecomment-1886138264

I hope this helps you finish running your samples, and if you continue to have problems, please let us know.

Kind Regards, Andre Sim