Dear Bambu team,
I am running a massive project with 480 BAM files with ~4.8 TB total data.
Following the previous suggestion for Bambu, I am running first the extended annotations (quant = FALSE), with the idea of running the quantification later in batches.
However, the is a major issue when starting the extended annotations:
--- Start extending annotations ---
Error in `vec_interleave_indices()`:
! Long vectors are not yet supported in `vec_interleave()`. Result from interleaving would have size 8857886400, which is larger than the maximum supported size of 2^31 - 1.
Backtrace:
▆
1. ├─bambu::bambu(...)
2. │ └─bambu:::bambu.extendAnnotations(...)
3. │ └─bambu:::isore.combineTranscriptCandidates(...)
4. │ ├─... %>% data.table()
5. │ └─bambu:::combineSplicedTranscriptModels(...)
6. │ └─bambu:::updateStartEndReadCount(combinedFeatureTibble)
7. │ └─... %>% mutate(sumReadCount = sum(readCount, na.rm = TRUE))
8. ├─data.table::data.table(.)
9. ├─dplyr::mutate(., sumReadCount = sum(readCount, na.rm = TRUE))
10. ├─dplyr::group_by(., rowID)
11. ├─tidyr::pivot_longer(...)
12. ├─tidyr:::pivot_longer.data.frame(...)
13. │ └─tidyr::pivot_longer_spec(...)
14. │ └─vctrs::vec_interleave(!!!val_cols, .ptype = val_type)
15. │ └─vctrs:::vec_interleave_indices(n, size)
16. └─rlang::abort(message = message)
Execution halted
Is there anything I could do to run Bambu?
My code looks like:
BAMlist = BAMs_one_per_Line
fa.file <- "/refData/release46/GRCh38.primary_assembly.genome.fa"
gtf.file <- "/refData/release46/gencode.v46.primary_assembly.annotation.gtf"
bambuAnnotations <- prepareAnnotations(gtf.file)
extendedAnnotations = bambu(reads = BAMlist, annotations = bambuAnnotations, genome = fa.file, quant = FALSE, lowMemory=T, ncore = 14, rcOutDir="MY_PATH/bambu_20241015_all")
As an additional note, I also have the same warning message as some others have reported as issue #407 .
This is with R 4.3.2 and Bioc 3.18 / bambu (3.4.1).
Platform: x86_64-conda-linux-gnu (64-bit)
All the best,
Niko
Dear Bambu team,
I am running a massive project with 480 BAM files with ~4.8 TB total data.
Following the previous suggestion for Bambu, I am running first the extended annotations (
quant = FALSE), with the idea of running the quantification later in batches.However, the is a major issue when starting the extended annotations:
Is there anything I could do to run Bambu?
My code looks like:
As an additional note, I also have the same warning message as some others have reported as issue #407 .
This is with R 4.3.2 and Bioc 3.18 / bambu (3.4.1).
Platform: x86_64-conda-linux-gnu (64-bit)
All the best,
Niko