Open Janelle555 opened 10 months ago
What does ./YA0442.1_2.intervals.pos.txt
look like? Does it have the same format as the example "pos" file?
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.
It should be tab separated, change it and let me know if it works
It should be tab separated, change it and let me know if it works
YEAH,it works! Thank you so much!
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?