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GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data
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BiocParallel error when putting multiple .bam files as inputs for reads #414

Open TingQi2020 opened 4 months ago

TingQi2020 commented 4 months ago

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 commented 4 months ago

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