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xmipp3-volume consensus fails #895

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mmmtnez opened this issue Jul 18, 2024 · 0 comments · May be fixed by #928
Open

xmipp3-volume consensus fails #895

mmmtnez opened this issue Jul 18, 2024 · 0 comments · May be fixed by #928
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@mmmtnez
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mmmtnez commented Jul 18, 2024

Hi,

the protocol xmipp3-volume consensus fails when I try to run the program with three maps included in boxes of 400 px and 1.1 A/px (pixel size):

Maps included in the input_volumes.txt file:
Runs/028887_ProtImportVolumes/extra/import_42773_relion_class001.mrc
Runs/028996_ProtImportVolumes/extra/import_43550_item2_relion_class001.mrc
Runs/028247_ProtImportVolumes/extra/import_41689_J79_001.mrc

The error is:

0001: Killed
00002: Traceback (most recent call last):
00003: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 203, in run
00004: self._run()
00005: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 254, in _run
00006: resultFiles = self._runFunc()
00007: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 250, in _runFunc
00008: return self._func(*self._args)
00009: File "/home/mmmtnz/miniconda/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_volume_consensus.py", line 66, in fusionStep
00010: self.runJob("xmipp_volume_consensus", args)
00011: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/protocol/protocol.py", line 1505, in runJob
00012: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00013: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/protocol/executor.py", line 65, in runJob
00014: process.runJob(log, programName, params,
00015: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/utils/process.py", line 56, in runJob
00016: return runCommand(command, env, cwd)
00017: File "/home/mmmtnz/software/scipion/scipion-pyworkflow/pyworkflow/utils/process.py", line 71, in runCommand
00018: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
00019: File "/home/mmmtnz/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
00020: raise CalledProcessError(retcode, cmd)
00021: subprocess.CalledProcessError: Command ' xmipp_volume_consensus -i Runs/032193_XmippProtVolConsensus/extra/input_volumes.txt -o Runs/032193_XmippProtVolConsensus/extra/consensus_volume.mrc' returned non-zero exit status 137.
00022: Protocol failed: Command ' xmipp_volume_consensus -i Runs/032193_XmippProtVolConsensus/extra/input_volumes.txt -o Runs/032193_XmippProtVolConsensus/extra/consensus_volume.mrc' returned non-zero exit status 137.

@MartinSalinas98 MartinSalinas98 added the bug Something isn't working label Sep 3, 2024
@oierlauzi oierlauzi linked a pull request Oct 22, 2024 that will close this issue
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