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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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AttributeError: 'module' object has no attribute 'Run' #27

Closed xmzhuo closed 3 years ago

xmzhuo commented 3 years ago

Arguments are: Query File: sample.theta2.interval_count k: 3 tau: 2 Output Directory: ./ Output Prefix: sample Num Processes: 1 Graph extension: .pdf Valid sample for THetA analysis: Ratio Deviation: 0.1 Min Fraction of Genome Aberrated: 0.05 Program WILL cluster intervals.

Reading in query file... Frac with potential copy numbers: 0.162949234132 Reading SNP file at sample.tumor.snp_formatted.txt Reading SNP file at sample.normal.snp_formatted.txt Reading interval file at sample.theta2.interval_count Calculating BAFs Determining heterozygosity. Calculating BAFs. First round of clustering... +++++++++++++++++++++++++++++ Traceback (most recent call last): File "/THetA/bin/../python/RunTHetA.py", line 514, in main() File "/THetA/bin/../python/RunTHetA.py", line 291, in main resultsfile2, boundsfile2 = run_fixed_N(2, args, intervals) File "/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 "/THetA/python/ClusteringBAF.py", line 99, in clustering_BAF metaData = generate_meta_data(intervals, byChrm, numProcesses, sampleName, generateData, outdir) File "/THetA/python/ClusteringBAF.py", line 152, in generate_meta_data results = p.map(cluster_wrapper, zip(intervals, linearizedSampleName, linearizedChrm, linearizedGenerateData)) File "/usr/lib/python2.7/multiprocessing/pool.py", line 253, in map return self.map_async(func, iterable, chunksize).get() File "/usr/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value AttributeError: 'module' object has no attribute 'Run'

The enbvironment: python 2.7.17 java: openjdk 11.0.11 2021-04-20 OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.18.04) OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.18.04, mixed mode, sharing)

packages: alabaster (0.7.12) asn1crypto (0.24.0) Babel (2.9.1) backports.functools-lru-cache (1.6.4) backports.shutil-get-terminal-size (1.0.0) bnpy (0.1.6, /bnpy) certifi (2020.12.5) chardet (4.0.0) cryptography (2.1.4) cycler (0.10.0) Cython (0.29.23) decorator (4.4.2) docutils (0.17.1) enum34 (1.1.6) idna (2.6) imagesize (1.2.0) ipaddress (1.0.17) ipython (5.10.0) ipython-genutils (0.2.0) Jinja2 (2.11.3) joblib (0.14.1) keyring (10.6.0) keyrings.alt (3.0) kiwisolver (1.1.0) MarkupSafe (1.1.1) matplotlib (2.2.5) memory-profiler (0.57.0) munkres (1.0.12) numexpr (2.7.3) numpy (1.16.6) packaging (20.9) pandas (0.24.2) pathlib2 (2.3.5) pexpect (4.8.0) pickleshare (0.7.5) Pillow (6.2.2) pip (9.0.1) prompt-toolkit (1.0.18) psutil (5.8.0) ptyprocess (0.7.0) pycrypto (2.6.1) Pygments (2.5.2) pygobject (3.26.1) pyparsing (2.4.7) python-dateutil (2.8.1) pytz (2021.1) pyxdg (0.25) requests (2.25.1) scandir (1.10.0) scikit-learn (0.20.4) scipy (1.2.3) SecretStorage (2.3.1) setuptools (39.0.1) simplegeneric (0.8.1) six (1.11.0) snowballstemmer (2.1.0) Sphinx (1.8.5) sphinx-gallery (0.4.0) sphinxcontrib-websupport (1.1.2) subprocess32 (3.5.4) traitlets (4.3.3) typing (3.10.0.0) urllib3 (1.26.4) wcwidth (0.2.5) wheel (0.30.0)

xmzhuo commented 3 years ago

the newer bnpy (installed with pip) cause the issue, as long as the older bnpy-dev (with git) was used, it works fine.