R -e 'library("STITCH"); STITCH(chr="NC_029266.1", bamlist="bamlist.txt",posfile="NC_029266.txt", outputdir="./", K=4, nGen=100, nCores=1)'
具体报错如下：
Loading required package: parallel
Loading required package: rrbgen
[2022-04-02 14:40:19] Running STITCH(chr = NC_029266.1, nGen = 100, posfile = NC_029266.txt, K = 4, S = 1, outputdir = ./, nStarts = , tempdir = NA, 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 = 1, 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 = NULL, 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)
[2022-04-02 14:40:19] Program start
[2022-04-02 14:40:19] Get and validate pos and gen
[2022-04-02 14:40:20] Done get and validate pos and gen
[2022-04-02 14:40:20] Get BAM sample names
[2022-04-02 14:40:23] Done getting BAM sample names
[2022-04-02 14:40:23] Generate inputs
Traceback:
1: cpp_read_reassign(ord = ord, qnameInteger_ord = qnameInteger_ord, bxtagInteger_ord = bxtagInteger_ord, bxtag_bad_ord = bxtag_bad_ord, qname = qname, bxtag = bxtag, strand = strand, sampleReadsRaw = sampleReadsRaw, readStart_ord = readStart_ord, readEnd_ord = readEnd_ord, readStart = readStart, readEnd = readEnd, iSizeUpperLimit = iSizeUpperLimit, bxTagUpperLimit = bxTagUpperLimit, use_bx_tag = use_bx_tag, save_sampleReadsInfo = save_sampleReadsInfo)
2: merge_reads_from_sampleReadsRaw(sampleReadsRaw = sampleReadsRaw, qname = qname, bxtag = bxtag, strand = strand, readStart = readStart, readEnd = readEnd, iSizeUpperLimit = iSizeUpperLimit, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit, save_sampleReadsInfo = save_sampleReadsInfo, qname_all = qname_all, readStart_all = readStart_all, readEnd_all = readEnd_all)
3: loadBamAndConvert(iBam = iBam, L = L, pos = pos, nSNPs = nSNPs, bam_files = bam_files, cram_files = cram_files, reference = reference, iSizeUpperLimit = iSizeUpperLimit, bqFilter = bqFilter, chr = chr, N = N, downsampleToCov = downsampleToCov, sampleNames = sampleNames, inputdir = inputdir, useSoftClippedBases = useSoftClippedBases, regionName = regionName, tempdir = tempdir, chrStart = chrStart, chrEnd = chrEnd, chrLength = chrLength, save_sampleReadsInfo = save_sampleReadsInfo, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit)
4: FUN(X[[i]], ...)
5: lapply(X = X, FUN = FUN, ...)
6: mclapply(1:length(sampleRanges), mc.cores = nCores, FUN = loadBamAndConvert_across_a_range, sampleRanges = sampleRanges, bundling_info = bundling_info, L = L, pos = pos, nSNPs = nSNPs, bam_files = bam_files, cram_files = cram_files, reference = reference, iSizeUpperLimit = iSizeUpperLimit, bqFilter = bqFilter, chr = chr, N = N, downsampleToCov = downsampleToCov, sampleNames = sampleNames, inputdir = inputdir, useSoftClippedBases = useSoftClippedBases, regionName = regionName, tempdir = tempdir, chrStart = chrStart, chrEnd = chrEnd, chrLength = chrLength, save_sampleReadsInfo = save_sampleReadsInfo, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit)
7: generate_input(bundling_info = bundling_info, L = L, pos = pos, nSNPs = nSNPs, bam_files = bam_files, cram_files = cram_files, reference = reference, iSizeUpperLimit = iSizeUpperLimit, bqFilter = bqFilter, chr = chr, N = N, downsampleToCov = downsampleToCov, sampleNames = sampleNames, inputdir = inputdir, useSoftClippedBases = useSoftClippedBases, regionName = regionName, tempdir = tempdir, chrStart = chrStart, chrEnd = chrEnd, nCores = nCores, save_sampleReadsInfo = save_sampleReadsInfo, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit)
8: generate_or_refactor_input(regenerateInput = regenerateInput, bundling_info = bundling_info, L = L, pos = pos, nSNPs = nSNPs, bam_files = bam_files, cram_files = cram_files, reference = reference, iSizeUpperLimit = iSizeUpperLimit, bqFilter = bqFilter, chr = chr, outputdir = outputdir, N = N, downsampleToCov = downsampleToCov, sampleNames = sampleNames, inputdir = inputdir, useSoftClippedBases = useSoftClippedBases, regionName = regionName, tempdir = tempdir, chrStart = chrStart, chrEnd = chrEnd, generateInputOnly = generateInputOnly, nCores = nCores, save_sampleReadsInfo = save_sampleReadsInfo, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit)
9: STITCH(chr = "NC_029266.1", bamlist = "bamlist.txt", posfile = "NC_029266.txt", outputdir = "./", K = 4, nGen = 100, nCores = 1)
An irrecoverable exception occurred. R is aborting now ...
/opt/gridengine/default/spool/njnode12/job_scripts/9133593: line 1: 63828 Segmentation fault (core dumped) ~/miniconda3/envs/R3.5/lib/R/bin/R -e 'library("STITCH"); STITCH(chr="NC_029266.1", bamlist="bamlist.txt",posfile="NC_029266.txt", outputdir="./", K=4, nGen=100, nCores=1)'