Error in process.y.margin.and.objective

[f-ferraro]

Hi,

I am trying to run bambu on kinnex data however I get the following error:

--- Start generating read class files ---
Pb1knn.filtered
Finished creating junction list with splice motif in 0 mins.
before strand correction, annotated introns: 22255 (0.249512299033567%)
after strand correction, annotated introns: 22267 (0.249646837231204)
Error: BiocParallel errors
  1 remote errors, element index: 1
  3 unevaluated and other errors
  first remote error:
Error in process.y.margin.and.objective(y, base_margin, objective, params): Got numeric 'y' - supported objectives for this data are: reg:squarederror, reg:squaredlogerror, reg:logistic, reg:pseudohubererror, reg:absoluteerror, reg:quantileerror, count:poisson, reg:gamma, reg:tweedie. Was passed: binary:logistic
In addition: Warning messages:
1: In bambu.processReadsByFile(bam.file = reads[bamFileName], genomeSequence = genomeSequence,  :
  not all chromosomes present in reference annotations, annotations might be incomplete. Please compare objects on the same reference
2: In bambu.processReadsByFile(bam.file = reads[bamFileName], genomeSequence = genomeSequence,  :
  911 reads are mapped outside the provided genomic regions. These reads will be dropped. Check you are using the same genome used for the alignment
3: In throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
4: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
5: In throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'label' has been renamed to 'y'. This warning will become an error in a future version.

I tried both with and without quantification and in and out of low memory modes, I always get the same issue.

> sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)

Matrix products: default
BLAS/LAPACK: /mnt/data/Pacbio-RNAseq/PacBio-Batch1_output/.pixi/envs/default/lib/libopenblasp-r0.3.30.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Amsterdam
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] bambu_3.8.3                 BSgenome_1.74.0
 [3] rtracklayer_1.66.0          BiocIO_1.16.0
 [5] Biostrings_2.74.0           XVector_0.46.0
 [7] SummarizedExperiment_1.36.0 Biobase_2.66.0
 [9] GenomicRanges_1.58.0        GenomeInfoDb_1.42.3
[11] IRanges_2.40.0              S4Vectors_0.44.0
[13] BiocGenerics_0.52.0         MatrixGenerics_1.18.0
[15] matrixStats_1.5.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.46.0          rjson_0.2.23             lattice_0.22-7
 [4] vctrs_0.6.5              tools_4.4.3              bitops_1.0-9
 [7] generics_0.1.4           curl_7.0.0               parallel_4.4.3
[10] tibble_3.3.0             AnnotationDbi_1.68.0     RSQLite_2.4.3
[13] blob_1.2.4               pkgconfig_2.0.3          Matrix_1.7-4
[16] data.table_1.17.8        lifecycle_1.0.4          GenomeInfoDbData_1.2.13
[19] compiler_4.4.3           Rsamtools_2.22.0         codetools_0.2-20
[22] RCurl_1.98-1.17          yaml_2.3.10              pillar_1.11.1
[25] crayon_1.5.3             tidyr_1.3.1              BiocParallel_1.40.0
[28] DelayedArray_0.32.0      cachem_1.1.0             abind_1.4-8
[31] tidyselect_1.2.1         purrr_1.1.0              dplyr_1.1.4
[34] restfulr_0.0.16          fastmap_1.2.0            grid_4.4.3
[37] cli_3.6.5                SparseArray_1.6.0        magrittr_2.0.4
[40] S4Arrays_1.6.0           GenomicFeatures_1.58.0   XML_3.99-0.17
[43] UCSC.utils_1.2.0         bit64_4.6.0-1            xgboost_3.0.5.1
[46] httr_1.4.7               bit_4.6.0                png_0.1-8
[49] memoise_2.0.1            rlang_1.1.6              Rcpp_1.1.0
[52] glue_1.8.0               DBI_1.2.3                jsonlite_2.0.0
[55] R6_2.6.1                 GenomicAlignments_1.42.0 zlibbioc_1.52.0

Any suggestion would be the most appreciated!
Thanks in advance.

[ch99l]

Hi,

Are you still facing this issue? To assist us with debugging this problem, would you be able to provide us the parameters you used when running bambu?

Thank you!

[number-25]

I was running basic bambu functions and encountering this exact same error running R version 4.5.2, installing the latest version of bambu from github (devtools)

grlist <- prepareAnnotations(annot_gtf)
se     <- bambu(reads = readlist, annotations = grlist, genome = genomeSequence, ncore = ncore, verbose = TRUE)
writeBambuOutput(se, output_tag)

What allowed me to avoid this error was to install an earlier xgboost version=1.7.7.1

Hope this helps.

[matteo-collina]

Thanks @number-25, that solution worked for me. I have R version 4.5.2 and bambu 3.12.0 installed.
However, some warnings about the xgboost still come out.