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Error while running bambu on multiple samples #513
Description
Hi,
I am running bambu on multiple samples, however, I come across an error. Could you please help me how to resolve this issue?
Since I am running bambu with multiple times, I tried processing annotation file first with annotations = prepareAnnotations(gtf.file) as well. I get same error.
Code:
library(bambu)
fa.file <- "/projects/hg38.fa"
gtf.file <- "/projects/gencode.v48.annotation.gtf"
DD1.bam.file <- "/projects/1_IsoSeqX_bc05_5p--IsoSeqX_3p.flnc.mapped.bam"
DD2.bam.file <- "/projects/2_IsoSeqX_bc01_5p--IsoSeqX_3p.flnc.mapped.bam"
DD3.bam.file <- "/projects/3_IsoSeqX_bc03_5p--IsoSeqX_3p.flnc.mapped.bam"
DD4.bam.file <- "/projects/4_IsoSeqX_bc04_5p--IsoSeqX_3p.flnc.mapped.bam"
DD5.bam.file <- "/projects/5_IsoSeqX_bc02_5p--IsoSeqX_3p.flnc.mapped.bam"
DD6.bam.file <- "/projects/6_IsoSeqX_bc08_5p--IsoSeqX_3p.flnc.mapped.bam"
DD7.bam.file <- "/projects/7_IsoSeqX_bc06_5p--IsoSeqX_3p.flnc.mapped.bam"
DD8.bam.file <- "/projects/8_IsoSeqX_bc07_5p--IsoSeqX_3p.flnc.mapped.bam"
DD9.bam.file <- "/projects/9_IsoSeqX_bc09_5p--IsoSeqX_3p.flnc.mapped.bam"
DD10.bam.file <- "/projects/10_IsoSeqX_bc10_5p--IsoSeqX_3p.flnc.mapped.bam"
se.multiSample <- bambu(reads = c(DD1.bam.file, DD2.bam.file, DD3.bam.file, DD4.bam.file, DD5.bam.file,
DD6.bam.file, DD7.bam.file, DD8.bam.file, DD9.bam.file, DD10.bam.file),
annotations = gtf.file, genome = fa.file)
Error:
Running Bambu-v3.9.0
If you are running bambu multiple times we recommend processing your annotation file first with annotations = prepareAnnotations(gtf.file)
--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://p3m.dev/cran/__linux__/jammy/2024-10-30
| | 0%Number of Read Classes - 686149
|============ | 10%Number of Read Classes - 764318
|======================== | 20%Number of Read Classes - 650238
|===================================== | 30%Number of Read Classes - 771976
|============================================================= | 50%
Error: BiocParallel errors
1 remote errors, element index: 5
5 unevaluated and other errors
first remote error:
Error in tibble(chr = as.factor(getChrFromGrList(readGrgList)), intronStarts = unname(unstrsplit(splitAsList(as.character(unlisted_junctions_start), : Tibble columns must have compatible sizes.
In addition: There were 26 warnings (use warnings() to see them)
Best Regards,
Toufiq
Activity
SuiYue-2308 commentedon Dec 8, 2025
Hi @Motoufiq
Could you let me know which branch you’re using? Also, are your data from single-cell experiments? This might be related to differences in BAM file formats.
Thanks!
Motoufiq commentedon Dec 8, 2025
@SuiYue-2308
Thank you for the response.
I installed in my
Rseveral months ago, and I don't exactly remember which branch I am using? I do see from my R, I am using bambuv3.11.1Is there a way to accurately know which branch I am using now?It is not from single-cell experiments. They are from
PacBiodata, and the samples are the bam files (Isoseq refine > mapped against hg38 reference using pbmm2 align, and sorted). I have 10 bam files in total and I am trying to run as multiple samples.Earlier, I tried importing all 10 bam files individually as well, out of 10, only one bam file, the 5th sample (i.e., DD5.bam.file) fails to import. Note this sample has twice the number of reads (~20M reads) compared to all other sample (bam) files. I could run other transcript collapsing tools such as
FLAIR,stringtie2etc., using this sample without any issues.Motoufiq commentedon Dec 11, 2025
@SuiYue-2308
I downloaded bambu from Bioconductor, and the bam file issue was resolved. However, I see my R shows bambu version 3.8.3 instead of version 3.12.0 (as shown in the Bioconductor)
The output of bambu also differs between the version.
version 3.11.1
version 3.8.3
SuiYue-2308 commentedon Dec 12, 2025
Hi,
Good to hear your issue has been resolved! We’ve updated bambu’s output format to better support single-cell data, where mtx files are more efficient. This change is only in the output format—the underlying readCount values should remain consistent with the previous format.
Thanks!
Motoufiq commentedon Dec 12, 2025
@SuiYue-2308 Noted, I believe the
extended_annotations.gtf content should also remain the same?SuiYue-2308 commentedon Jan 7, 2026
Hi,
There will be some small changes, but most transcripts in extended_annotations.gtf will remain the same. We’re just aiming to identify additional novel isoforms that we couldn’t detect before.
Thanks!