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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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Child process exited with exitcode=1. Aborting. #90

Open GaoChengyu opened 2 years ago

GaoChengyu commented 2 years ago

Hi I use ipdSummary to detect 6ma. but i meet a error. Process KineticWorkerProcess-4: Traceback (most recent call last): File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/kineticsTools-0.8.0-py3.9-linux-x86_64.egg/kineticsTools/WorkerProcess.py", line 151, in run self._run() File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/kineticsTools-0.8.0-py3.9-linux-x86_64.egg/kineticsTools/WorkerProcess.py", line 127, in _run result = self.onChunk( # pylint: disable=assignment-from-none File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/kineticsTools-0.8.0-py3.9-linux-x86_64.egg/kineticsTools/KineticWorker.py", line 121, in onChunk perSiteResults = self._summarizeReferenceRegion( File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/kineticsTools-0.8.0-py3.9-linux-x86_64.egg/kineticsTools/KineticWorker.py", line 230, in _summarizeReferenceRegion (caseChunks, capValue) = self._fetchChunks( File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/kineticsTools-0.8.0-py3.9-linux-x86_64.egg/kineticsTools/KineticWorker.py", line 432, in _fetchChunks hits = np.random.choice( File "mtrand.pyx", line 901, in numpy.random.mtrand.RandomState.choice File "/home/gaocy/miniconda3/envs/genome/lib/python3.9/site-packages/pbcore-2.4.0-py3.9.egg/pbcore/io/align/BamAlignment.py", line 68, in f raise UnavailableFeature( pbcore.io.align._BamSupport.UnavailableFeature: this feature requires a PacBio BAM index [INFO] 2022-01-15 07:26:46,816Z [root _run 125] Got chunk: (33061, ReferenceWindow(refId=7, refName='scaffold8', start=2345000, end=2346000)) -- Process: <KineticWorkerProcess name='KineticWorkerProcess-5' parent=13610 started daemon> [INFO] 2022-01-15 07:26:46,833Z [root _summarizeReferenceRegion 226] Making summary: 2344985 to 2346015 Child process exited with exitcode=1. Aborting. My genome fasta file has 36 contigs. When i use ipdSummary to detect contig1 to contig7, everything is OK. but when ipdSummary run contig 8, the error occurred. Maybe i can get help from you. thank you very much!

liuweiming1 commented 2 months ago

Hello, have you solved this problem?