I'm running GLIMPSE2 on low pass WGS data from cats (Felis catus) with a custom imputation panel. I've run well over a thousand samples through this panel, and have run into a couple of samples recently where GLIMPSE2 is failing, and I can't tell why. It would appear that it just exits without a clear message during the first burn-in iteration. I've attached a log output below .. there's no output after the last line at all.
I'll note that this panel was built from just under 1,000 cats, so there are indeed less than 2,000 haplotypes in the reference panel, and so I'm interpreting No PBWT selection (Kpbwt=0 or Kpbwt >= n_ref_haps) as normal, and not indicative of an error.
I would greatly appreciate any guidance on how to diagnose what's going on with this particular sample. Thanks!
[GLIMPSE2] Phase and impute low coverage sequencing data
* Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne
* Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch
* Version : GLIMPSE2_phase v2.0.0 / commit = 2.0.1 / release = 2024-12-15
* Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213
* : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0
* Run date : 25/03/2026 - 16:27:42
Files:
* Input BAM/CRAM : [<redacted>.bam]
* Reference binary : [<redacted>.bin]
* Output file : [chrB2_82907913_95564380.bcf]
* Output format : [BCF format | ZLIB compression]
GLIMPSE_phase parameters:
* Imputation model : [Reference panel imputation]
* Input region : [Given by binary reference panel]
* Output region : [Given by binary reference panel]
* Sparse MAF : [Given by binary reference panel]
* Recombination rates : [Given by binary reference panel]
* Ploidy : [Only diploid samples in region]
* Keep monom. ref sites: [NO]
Model parameters:
* #Burnin iterations : [5]
* #Main iterations : [15]
* Ne [eff. pop. size] : [100000]
* Phase error rate : [0.0001]
* Imputation error rate: [1e-12]
* Min value for hap GLs: [1e-10]
Selection parameters:
* K init : [1000]
* K pbwt : [2000]
* PBWT depth : [12]
* PBWT modulo (cM) : [0.1]
* State list : [No list provided]
Genotype calling:
* Calling model : [standard]
* Perform calling]
BAM/CRAM filters and options:
* Min mapping quality : [10]
* Min base quality : [10]
* Max depth : [40]
* Keep failed QC : [NO]
* Keep orphan reads : [NO]
* Keep duplicate reads : [NO]
* Keep supp. alignment : [NO]
* Check pairing : [NO]
* Ignore orientation : [NO]
* Illumina-1.3+ : [NO]
Other parameters
* Seed : [15052011]
* #Threads : [1]
Initialisation:
* Binary reference panel parsing ...
* Binary reference panel parsing [done] (0.57s)
* Binary reference panel [Nrh=1964] [L=482497] [Lrare= 0 (0.0%) - Lcommon= 482497 (100.0%)]
* Input region : [chrB2:82907913-95564380]
* Output region : [chrB2:83759094-93502836]
* Sparse MAF : [0.001]
* Reading BAM files
* Reading BAM files [100%]
* Reading BAM files done (0.44s)
* Coverage statistics reported in: [chrB2_82907913_95564380_stats_coverage.txt.gz]
* Avg. sequencing coverage: 0.239979
* RARE transpose Ref (0.00s)
* Region spans 12656468 bp and 8.35 cM
* No PBWT allocated (Kpbwt=0 or Kpbwt >= n_ref_haps)
Initializing iteration
* Init rare Tar [#non-ref gls: 0] (0.00s)
* HMM imputation [#states=1000.0 / %poly=100.0%] (8.68s)
Burn-in iteration [1/5]
* HAP update Tar (0.00s)
* RARE transpose Tar (0.00s)
* No PBWT selection (Kpbwt=0 or Kpbwt >= n_ref_haps)
I'm running GLIMPSE2 on low pass WGS data from cats (Felis catus) with a custom imputation panel. I've run well over a thousand samples through this panel, and have run into a couple of samples recently where GLIMPSE2 is failing, and I can't tell why. It would appear that it just exits without a clear message during the first burn-in iteration. I've attached a log output below .. there's no output after the last line at all.
I'll note that this panel was built from just under 1,000 cats, so there are indeed less than 2,000 haplotypes in the reference panel, and so I'm interpreting
No PBWT selection (Kpbwt=0 or Kpbwt >= n_ref_haps)as normal, and not indicative of an error.I would greatly appreciate any guidance on how to diagnose what's going on with this particular sample. Thanks!