BiocParallel errors

[abhijitcbio]

Hi,

I am trying to process 18 samples but getting the following error -

Error: BiocParallel errors
  1 remote errors, element index: 1
  17 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: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Here is my code

library(bambu)

gtf.file <- "../../../genome/Homo_sapiens.GRCh38.111.gtf"
fa.file  <- "../../../genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
annotations <- prepareAnnotations(gtf.file)

se <- bambu(reads = c(
"../bam/P272_nCD4.bam",
"../bam/P293_nCD4.bam",
"../bam/P295_nCD4.bam",
"../bam/P303_nCD4.bam",
"../bam/P314_nCD4.bam",
"../bam/P317_nCD4.bam",
"../bam/P319_nCD4.bam",
"../bam/P322_nCD4.bam",
"../bam/P332_nCD4.bam",
"../bam/P333_nCD4.bam",
"../bam/P336_nCD4.bam",
"../bam/P342_nCD4.bam",
"../bam/P343_nCD4.bam",
"../bam/P354_nCD4.bam",
"../bam/P358_nCD4.bam",
"../bam/P367_nCD4.bam",
"../bam/P370_nCD4.bam",
"../bam/P373_nCD4.bam"
), annotations = annotations, genome = fa.file, discovery = TRUE, quant = TRUE, lowMemory = TRUE, ncore = 1, verbose = TRUE)

writeBambuOutput(se, ".", prefix="nCD4_transcriptome")
saveRDS(se, paste0("nCD4_transcriptome.rds"))

For your reference, I have attached the full log.

Looking forward to your help.

log.txt

[cying111]

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

[tdfy]

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

[SuhasSrinivasan]

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.