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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Assertion error during experimentWrapper.py #122

Open stlomo opened 3 years ago

stlomo commented 3 years ago

Hello

I`m running a very small run on to test progressive cactus using yeast mithocondrial genomes, the pipeline works up to a point in which the following error shows up (I include for completeness the entire TOIL output log)

[2020-12-10T15:13:00+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2020-12-10T15:13:00+0100] [MainThread] [I] [toil] Running Toil version 4.2.0-3aa1da130141039cb357efe36d7df9b9f6ae9b5b on host pcsy384. [2020-12-10T15:13:02+0100] [MainThread] [I] [cactus.progressive.cactus_progressive] Progressive Up: 0.000000 [2020-12-10T15:13:02+0100] [MainThread] [I] [cactus.progressive.cactus_progressive] Sequences in progressive, 0.000000: ['Saccharomyces_mikatae', 'Saccharomyces_paradoxus', 'Saccharomyces_cerevisiae'] ('setting this', 'Saccharomyces_mikatae', 'files/for-job/kind-MergeChunks2/instance-mue9xdf3/file-8s94gbt3/tmpiyed5l8l.tmp') ('setting this', 'Saccharomyces_paradoxus', 'files/for-job/kind-MergeChunks2/instance-o171her9/file-t35gbvzw/tmp4jxyd7ti.tmp') Traceback (most recent call last): File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/toil/worker.py", line 368, in workerScript job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/cactus/shared/common.py", line 1369, in _runner super(RoundedJob, self)._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/toil/job.py", line 1424, in _runner returnValues = self._run(jobGraph, fileStore) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/toil/job.py", line 1361, in _run return self.run(fileStore) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/cactus/progressive/cactus_progressive.py", line 189, in run workFlowArgs = CactusWorkflowArguments(self.options, experimentFile=experimentFile, configNode=configNode, seqIDMap = seqIDMap) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/cactus/pipeline/cactus_workflow.py", line 1378, in init self.experimentWrapper.setSequenceID(genome, seqID) File "/mnt/d/CACTUS/cactus-bin-v1.2.3/venv/lib/python3.8/site-packages/cactus/shared/experimentWrapper.py", line 354, in setSequenceID assert len(genomeNodes) == 1 AssertionError [2020-12-10T15:13:02+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host pcsy384

Any advice on what is causing this? Thank you

Jome0169 commented 3 years ago

Hi @stlomo, did you ever solve this issue? I appear to be getting a similar error and am having a hard time backtracing the root cause.