Assembling haplotypesError in indices[, 2] : incorrect number of dimensions

[YichaoOU]

Hi,

I got this error as part of the mosaicatcher snakemake pipeline using my own data. I didn't see this problem when using the public data.

Error in rule run_strandphaser_per_chrom:
    jobid: 429
    output: strand_states/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/StrandPhaseR_analysis.chr17/Phased/phased_haps.txt, strand_states/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/StrandPhaseR_analysis.chr17/VCFfiles/chr17_phased.vcf
    log: log/run_strandphaser_per_chrom/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/chr17.log (check log file(s) for error message)
    shell:
        
        Rscript utils/StrandPhaseR_pipeline.R                 bam/GFP_BAF/selected                 strand_states/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/StrandPhaseR_analysis.chr17                 strand_states/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/StrandPhaseR.chr17.config                 strand_states/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/strandphaser_input.txt                 snv_calls/GFP_BAF/chr17.vcf                 $(pwd)/utils/R-packages/                 > log/run_strandphaser_per_chrom/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/chr17.log 2>&1

log/run_strandphaser_per_chrom/GFP_BAF/100000_fixed_norm.selected_j0.1_s0.5_scedist20/chr17.lo

Loading VCF file ... 0.43s
Working on chromosome chr17
 Loading data for 11 WCregions 54.14s
  Sorting matrices: iteration 1 3.88s
  Sorting matrices: iteration 2 4.11s
 Assembling haplotypesError in indices[, 2] : incorrect number of dimensions
Calls: strandPhaseR ... phaseChromosome -> assembleHaps -> exportConsensus -> split
In addition: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 11 out-of-bound ranges located on sequence
  chr17. Note that only ranges located on a non-circular sequence whose
  length is not NA can be considered out-of-bound (use seqlengths() and
  isCircular() to get the lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.
Execution halted

Any solutions?

Thanks,
Yichao