BiocParallel errors #468

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1. cying111 commented on Apr 3, 2025

   

   cying111

   on Apr 3, 2025

   Collaborator

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   Hi @abhijitcbio ,

   Sorry for the delayed response.

   The log file shows several samples with zero read counts, which could be due to a mismatch between the gtf/fasta and bam file (e.g., seqlevel styles) or the samples genuinely having no reads.

   To proceed, please ensure:

   • the same fasta file is used for alignment.

   • gtf and the fasta file match.

   • empty bam files are filtered out so bambu can process them properly.

   Hope this helps! Let us know if you have any questions.
   Thank you
   Ying
2. tdfy commented on Sep 23, 2025

   

   tdfy

   on Sep 23, 2025

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   hello,

   I have rec'd a similar error. I can confirm the same ref fa was used for alignment and bam files are in order.

   I downloaded primary assembly hg fa and gtf from GENCODE. I noticed the 'chromosome' convention varies between the ref fa and gtf. For example; 'chr1 1, chr2 2, ..' (fa) vs 'chr1, chr2,..' (gtf).

   Would this account for the error below? I also noticed more scaffolds in the fa compared to gtf.

   Thanks!

   -Todd

   Error: BiocParallel errors
     1 remote errors, element index: 1
     0 unevaluated and other errors
     first remote error:
   Error in matrix(mcols(exonsByRC)$readCount, dimnames = list(names(exonsByRC), : 'data' must be of a vector type, was 'NULL'
   In addition: Warning messages:
   1: In findHighConfidenceJunctions(junctions = uniqueJunctions, junctionModel = junctionModel,  :
     no junction correction as no high confidence reference junctions found
   2: In findHighConfidenceJunctions(junctions = uniqueJunctions, junctionModel = junctionModel,  :
     no junction correction as no high confidence reference junctions found
   3: In findHighConfidenceJunctions(junctions = uniqueJunctions, junctionModel = junctionModel,  :
     no junction correction as no high confidence reference junctions found
   4: In findHighConfidenceJunctions(junctions = uniqueJunctions, junctionModel = junctionModel,  :
     no junction correction as no high confidence reference junctions found
   Execution halted
   
3. SuhasSrinivasan commented on Dec 15, 2025

   

   SuhasSrinivasan

   on Dec 15, 2025

   Last edited by SuhasSrinivasan

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   Hi @cying111 ,

   This issue is present in the current Bioconductor version: v3.12

   Trying to test on a single BAM file, the BAM file is sorted and indexed.

   The Genome FASTA file and GTF file are GENCODE v48.

   prp_anno <- prepareAnnotations(gtf_file)
   
   se_test <- bambu(
       reads = test_sample,
       annotations = prp_anno,
       genome = fa_file,
       ncore = cpu_cores,
       verbose = TRUE
   )

   Finished creating transcript models (read classes) for reads with spliced junctions in 0 mins.
   Finished create single exon transcript models (read classes) in 0.5 mins.
   Error: BiocParallel errors
     1 remote errors, element index: 1
     0 unevaluated and other errors
     first remote error:
   Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
   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,  :
     3343 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 bambu.processReadsByFile(bam.file = reads[bamFileName], genomeSequence = genomeSequence,  :
     No aligned spliced reads detected!Bambu expects spliced reads. If this is intended, see Documentation on how to handle single-exon transcripts
   Execution halted
   

   Can we please receive some guidance on why these errors are occurring?
   Thank you for your consideration.