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raphael-group / THetA

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
http://compbio.cs.brown.edu/projects/theta/
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Assertion error when having SNP inputs #25

Open YY-SONG0718 opened 3 years ago

YY-SONG0718 commented 3 years ago

Dear maintainer,

I am experiencing an assertion error when running THetA2. This error only happens when I give --TUMOR_FILE and --NORMAL_FILE.

Without these inputs and only use interval count files, the program ran well. Testing the pipeline using files in THetA/example worked well too. 

Traceback (most recent call last):
  File "/bnpy-dev/THetA/bin/../python/RunTHetA.py", line 514, in <module>
    main()
  File "/bnpy-dev/THetA/bin/../python/RunTHetA.py", line 291, in main
    resultsfile2, boundsfile2 = run_fixed_N(2, args, intervals)
  File "/bnpy-dev/THetA/bin/../python/RunTHetA.py", line 328, in run_fixed_N
    lengths, tumorCounts, normalCounts, m, upper_bounds, lower_bounds, clusterAssignments, numClusters, clusterMeans, normalInd = clustering_BAF(n, intervals=intervals, missingData=missingData, prefix=prefix, outdir=directory, numProcesses=num_processes)
  File "/bnpy-dev/THetA/python/ClusteringBAF.py", line 106, in clustering_BAF
    metaMu, metaSigma, clusterAssignments, numPoints, numClusters = cluster(metaData, sampleName, sf=0.01, intervals=intervals)
  File "/bnpy-dev/THetA/python/ClusteringBAF.py", line 263, in cluster
    Data = format_data(data, sampleName, chrm)
  File "/bnpy-dev/THetA/python/ClusteringBAF.py", line 306, in format_data
    Data = bnpy.data.XData(X=npArray)
  File "/bnpy-dev/bnpy/data/XData.py", line 97, in __init__
    self._check_dims()
  File "/bnpy-dev/bnpy/data/XData.py", line 121, in _check_dims
    assert self.X.flags.owndata
AssertionError

Here is an example of my --TUMOR_FILE, tab-separated:

Chrm Pos Ref_Allele Mut_Allele

1 1370651 24 5 1 2473951 37 4 1 3015890 20 5 1 3131698 40 3 1 4045065 18 5 1 4384916 26 4 1 4465499 29 5 1 4600606 27 3 1 4714444 41 4

I suspect that it is an issue related to the above input, but I cannot see the difference between mine and the example file. May I ask that what is the assertion for and what should I do?

Many thanks in advance.

Kind regards,

Yuyao

matinslh commented 11 months ago

Dear Yuyao,

Were you able to solve the problem?

Best, Matin