Error: Execution halted

[Janelle555]

Hi,
I got this error when runing STITCH:
'''
[2023-12-05 20:59:19] Running STITCH(chr = 1, nGen = 100, posfile =./YA0442.1_2.intervals.pos.txt, K = 10, S = 1, outputdir =./CHR1_SNP, nStarts = , tempdir = ./STITCH/temp/, bamlist = bamlist.txt, cramlist = , sampleNames_file = , reference = , genfile = , method = diploid, output_format = bgvcf, B_bit_prob = 16, outputInputInVCFFormat = FALSE, downsampleToCov = 50, downsampleFraction = 1, readAware = TRUE, chrStart = NA, chrEnd = NA, regionStart = NA, regionEnd = NA, buffer = NA, maxDifferenceBetweenReads = 1000, maxEmissionMatrixDifference = 1e+10, alphaMatThreshold = 1e-04, emissionThreshold = 1e-04, iSizeUpperLimit = 600, bqFilter = 17, niterations = 40, shuffleHaplotypeIterations = c(4, 8, 12, 16), splitReadIterations = 25, nCores = 60, expRate = 0.5, maxRate = 100, minRate = 0.1, Jmax = 1000, regenerateInput = TRUE, originalRegionName = NA, keepInterimFiles = FALSE, keepTempDir = FALSE, outputHaplotypeProbabilities = FALSE, switchModelIteration = NA, generateInputOnly = FALSE, restartIterations = NA, refillIterations = c(6, 10, 14, 18), downsampleSamples = 1, downsampleSamplesKeepList = NA, subsetSNPsfile = NA, useSoftClippedBases = FALSE, outputBlockSize = 1000, outputSNPBlockSize = 10000, inputBundleBlockSize = NA, genetic_map_file = , reference_haplotype_file = , reference_legend_file = , reference_sample_file = , reference_populations = NA, reference_phred = 20, reference_iterations = 40, reference_shuffleHaplotypeIterations = c(4, 8, 12, 16), output_filename = YA0442.1_2.intervals.SNP.mark.vcf.gz, initial_min_hapProb = 0.2, initial_max_hapProb = 0.8, regenerateInputWithDefaultValues = FALSE, plotHapSumDuringIterations = FALSE, plot_shuffle_haplotype_attempts = FALSE, plotAfterImputation = TRUE, save_sampleReadsInfo = FALSE, gridWindowSize = NA, shuffle_bin_nSNPs = NULL, shuffle_bin_radius = 5000, keepSampleReadsInRAM = FALSE, useTempdirWhileWriting = FALSE, output_haplotype_dosages = FALSE, use_bx_tag = TRUE, bxTagUpperLimit = 50000)
[2023-12-05 20:59:19] Program start
[2023-12-05 20:59:19] Get and validate pos and gen
Error in names(x) <- value :
'names' attribute [4] must be the same length as the vector [1]
Calls: STITCH ... get_and_validate_pos_gen_and_phase -> get_and_validate_pos -> colnames<-
Execution halted
'''
Sincerely ask: What is the cause of this error?

[rwdavies]

What does ./YA0442.1_2.intervals.pos.txt look like? Does it have the same format as the example "pos" file?

[Janelle555]

What does ./YA0442.1_2.intervals.pos.txt look like? Does it have the same format as the example "pos" file?
The format of the posfile file looks like this:
1 1364 C G
1 1973 G T
1 2001 G T
1 2862 G T
1 3175 A T
1 3188 G T
1 3210 A T
1 3223 C A
1 3264 T A
1 4553 A G
1 4570 C A
1 4611 C T
1 5730 C A
All four columns are the same length.

[rwdavies]

It should be tab separated, change it and let me know if it works

[Janelle555]

It should be tab separated, change it and let me know if it works

YEAH，it works! Thank you so much!