When using QUILT2.R to impute downsampled data with the gold standard file as the reference panel, an issue occurs.

[bbdragon1]

Hi，
The program only generates chunked panel data as RData files but does not proceed to the imputation step. When using a different reference panel with the same code, there are no issues; only the panel file is different. I have confirmed that the buffer, imputation start, and end position information are correct. I would like to understand why this happens and seek assistance. Here is my code：
QUILT2_PATH="QUILT2.R"
$QUILT2_PATH
--outputdir="$Output_dir"
--chr="$chrom"
--nCores="$Threads_num"
--regionStart="$regionStart"
--regionEnd="$regionEnd"
--buffer="$buffer"
--nGen=100
--bamlist="$Bamlist"
--reference_vcf_file="$Panel_file"
--save_prepared_reference=TRUE

[Zilong-Li]

Hey,

Can you show the log? Also, make sure you are re-running the command with different outputdir.

[bbdragon1]

Hello, I have noticed the following error when running files, but I am not sure what the reason for this error is :
Error in mtm[!x, ] : (subscript) logical subscript too long
Calls: QUILT ... select_new_haps_mspbwt_v3 -> lapply -> FUN -> lapply -> FUN
Execution halted
Command exited with non-zero status 1. I would like to ask for your help.
The following is the log content:
[2024-11-10 10:01:37] Running QUILT(outputdir = gold_82_25_panel_preared_chr1_quilt2_output, chr = 1, method = diploid, regionStart = 1, regionEnd = 8000000, buffer = 500000, fflist = , bamlist = /..../bam/lcWGS_downsample_bam.list, cramlist = , sampleNames_file = , reference = , nCores = 1, nGibbsSamples = 7, n_seek_its = 3, n_burn_in_seek_its = NA, Ksubset = 600, Knew = 600, K_top_matches = 5, output_gt_phased_genotypes = TRUE, heuristic_match_thin = 0.1, output_filename = NULL, RData_objects_to_save = NULL, output_RData_filename = NULL, prepared_reference_filename = gold_82_25_panel_preared_chr1_quilt2_output/RData/QUILT_prepared_reference.1.1.8000000.RData, save_prepared_reference = FALSE, tempdir = NA, bqFilter = 17, panel_size = NA, posfile = , genfile = , phasefile = , maxDifferenceBetweenReads = 1e+10, make_plots = FALSE, make_plots_block_gibbs = FALSE, verbose = TRUE, shuffle_bin_radius = 5000, iSizeUpperLimit = 1e+06, record_read_label_usage = FALSE, record_interim_dosages = FALSE, use_bx_tag = TRUE, bxTagUpperLimit = 50000, addOptimalHapsToVCF = FALSE, estimate_bq_using_truth_read_labels = FALSE, override_default_params_for_small_ref_panel = TRUE, gamma_physically_closest_to = NA, seed = NA, hla_run = FALSE, downsampleToCov = 30, minGLValue = 1e-10, minimum_number_of_sample_reads = 2, nGen = 100, reference_vcf_file = , reference_haplotype_file = , reference_legend_file = , reference_sample_file = , reference_populations = NA, reference_phred = 30, reference_exclude_samplelist_file = , region_exclude_file = , genetic_map_file = , nMaxDH = NA, make_fake_vcf_with_sites_list = FALSE, output_sites_filename = NA, expRate = 1, maxRate = 100, minRate = 0.1, print_extra_timing_information = FALSE, small_ref_panel_block_gibbs_iterations = c(3, 6, 9), small_ref_panel_gibbs_iterations = 20, plot_per_sample_likelihoods = FALSE, use_small_eHapsCurrent_tc = FALSE, mspbwtL = 3, mspbwtM = 1, use_mspbwt = TRUE, mspbwt_nindices = 4, use_splitreadgl = FALSE, override_use_eMatDH_special_symbols = NA, use_hapMatcherR = TRUE, shard_check_every_pair = TRUE, use_eigen = TRUE, impute_rare_common = TRUE, rare_af_threshold = 0.001, make_heuristic_plot = FALSE, heuristic_approach = A, use_list_of_columns_of_A = TRUE, calculate_gamma_on_the_fly = TRUE)
[2024-11-10 10:01:37] Auto-set n_burn_in_seek_its to 2 i.e. only sample one dosage per Gibbs sample
[2024-11-10 10:01:37] Overriding default parameters for small reference panel
[2024-11-10 10:01:37] Observing number of reference haplotypes K=164
[2024-11-10 10:01:37] Reset n_seek_its from 3 to 1
[2024-11-10 10:01:37] Reset n_burn_in_seek_its from 2 to 0
[2024-11-10 10:01:37] Set Ksubset to 164 (no longer necessary)
[2024-11-10 10:01:37] Set Knew to 164 (no longer necessary)
[2024-11-10 10:01:37] Get BAM sample names
[2024-11-10 10:01:37] Done getting BAM sample names
[2024-11-10 10:01:37] There are 359 common SNPs and 359 SNPs overall in this region
[2024-11-10 10:01:37] There are 0 regions out of 11 below minimum recombination rate, setting them to minimum rate
[2024-11-10 10:01:37] There are 0 regions out of 11 above maximum recombination rate, setting them to maximum rate
[2024-11-10 10:01:37] Imputing sample: 1
[W::hts_idx_load3] The index file is older than the data file: /home/zhangz_group/zhangz4/data/USER/zhongzm/Me2/LcWGS/bam/P67C08.downsample.bam.bai
[W::hts_idx_load3] The index file is older than the data file: /home/zhangz_group/zhangz4/data/USER/zhongzm/Me2/LcWGS/bam/P67C08.downsample.bam.bai
[2024-11-10 10:01:50] The average depth of this sample is:1.41442521399119
[2024-11-10 10:01:50] There are 166 reads under consideration
[2024-11-10 10:01:50] i_gibbs=1, i_it = 1 small gibbs
[2024-11-10 10:01:50] i_gibbs=1, i_it = 1 full
Error in mtm[!x, ] : (subscript) logical subscript too long
Calls: QUILT ... select_new_haps_mspbwt_v3 -> lapply -> FUN -> lapply -> FUN
Execution halted
Command exited with non-zero status 1
Command being timed: "QUILT2.R --prepared_reference_filename=gold_82_25_panel_preared_chr1_quilt2_output/RData/QUILT_prepared_reference.1.1.8000000.RData --bamlist=/..../bam/lcWGS_downsample_bam.list --chr=1 --method=diploid --nCores=1 --regionStart=1 --regionEnd=8000000 --buffer=500000 --nGen=100 --outputdir=gold_82_25_panel_preared_chr1_quilt2_output"
User time (seconds): 13.19
System time (seconds): 0.37
Percent of CPU this job got: 99%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:13.58
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 691164
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 135628
Voluntary context switches: 299
Involuntary context switches: 53
Swaps: 0
File system inputs: 337752
File system outputs: 16
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 1

[Zilong-Li]

Hi,

Seems you have a small reference panel of 164 haplotypes. And we recommend to use QUILT1 for small reference panel. Also, we had a new release v2.0.1 which may fix some errors for small reference panel. Can you also try it? Let us know it helps.

Best,
Zilong.

[bbdragon1]

Thank you for answering my questions. We will continue testing with version 2.0.1 next. Thank you for your help.