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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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progressive_schedule fails #132

Open vpymerel opened 1 year ago

vpymerel commented 1 year ago

Hello !

I am trying to use cactus (docker) to align ~10 insects genomes and I got the following error for job 'progressive_schedule' :

---[2022-10-30T02:45:26+0200] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker progressive_schedule file:/scratch/vmerel/WGA/Cactus/LG6/jobStore kind-progressive_schedule/instance-_9ny79_l. [2022-10-30T02:45:26+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'progressive_schedule' kind-progressive_schedule/instance-_9ny79_l v1 Exit reason: None [2022-10-30T02:45:26+0200] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'progressive_schedule' kind-progressive_schedule/instance-_9ny79_l v2 [2022-10-30T02:45:26+0200] [MainThread] [W] [toil.leader] Log from job "kind-progressive_schedule/instance-_9ny79_l" follows: =========> [2022-10-30T02:45:26+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2022-10-30T02:45:26+0200] [MainThread] [I] [toil] Running Toil version 5.7.1-b5cae9634820d76cb6c13b2a6312895122017d54 on host dna068. [2022-10-30T02:45:26+0200] [MainThread] [I] [toil.worker] Working on job 'progressive_schedule' kind-progressive_schedule/instance-_9ny79_l v1 [2022-10-30T02:45:26+0200] [MainThread] [I] [toil.worker] Loaded body Job('progressive_schedule' kind-progressive_schedule/instance-_9ny79_l v1) from description 'progressive_schedule' kind-progressive_schedule/instance-_9ny79_l v1 Traceback (most recent call last): File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/worker.py", line 407, in workerScript job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2406, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2324, in _run return self.run(fileStore) File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2547, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/cactus/cactus_env/lib/python3.10/site-packages/cactus/progressive/cactus_progressive.py", line 147, in progressive_schedule raise RuntimeError("Unable to schedule job dependencies. Please file a bug report on github") RuntimeError: Unable to schedule job dependencies. Please file a bug report on github [2022-10-30T02:45:26+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host dna068 <=========

Can you help me please ?

Thank you ! V

glennhickey commented 1 year ago

Can you please share your input tree?

vpymerel commented 1 year ago

Yes sure,

Here it is: (BGIGI:0.216097,(((TGE_A:0.00174569,TGE_H20:0.0018409):0.00325768,TPA:0.00711254):0.0110921,(((TCM:0.00370156,TSI:0.00335399):0.00562986,(TDI:0.00349392,TPS:0.0069705):0.00518438):0.0073258,(TCE:0.0131574,TMS:0.00461954):0.00878047):0.00799635)TIMEMA:0.186162);

--root TIMEMA

Thank you !