glennhickey
commented
2 months ago When you see Killed that generally means the job was stopped by your system due to using too much memory.
Open jallen73 opened 2 months ago
glennhickey
commented
2 months ago When you see Killed that generally means the job was stopped by your system due to using too much memory.
I've spent most of the day now trying to get cactus to run and I keep getting errors. I've tried uninstalling and reinstalling it. When I run it on the test data it works well, but I can't seem to get it to run on my data. Would definitely appreciate some insight here.
THE FIRST ERROR: [2024-08-27T16:24:01-0700] [MainThread] [I] [toil-rt] cactus_consolidated(0.62587): Killed [2024-08-27T16:24:02-0700] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker cactus_cons file:/mnt/c/Users/jessi/Documents/tools/cactus/jobstore kind-cactus_cons/instance-084c0khg. [2024-08-27T16:24:02-0700] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'cactus_cons' kind-cactus_cons/instance-084c0khg v1 Exit reason: None [2024-08-27T16:24:02-0700] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'cactus_cons' kind-cactus_cons/instance-084c0khg v2 [2024-08-27T16:24:02-0700] [MainThread] [W] [toil.leader] Log from job "kind-cactus_cons/instance-084c0khg" follows:
THE LAST ERROR: [2024-08-27T16:27:30-0700] [MainThread] [C] [toil.worker] Worker crashed with traceback: Traceback (most recent call last): File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/toil/worker.py", line 438, in workerScript job._runner(jobGraph=None, jobStore=job_store, fileStore=fileStore, defer=defer) File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2984, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2895, in _run return self.run(fileStore) File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 3158, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/cactus/pipeline/cactus_workflow.py", line 148, in cactus_cons messages = cactus_call(check_output=True, returnStdErr=True, File "/mnt/c/Users/jessi/Documents/tools/cactus/cactus_env/lib/python3.10/site-packages/cactus/shared/common.py", line 910, in cactus_call raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out)) RuntimeError: cactus_consolidated(0.6139): Command ['docker', 'run', '--interactive', '--net=host', '--log-driver=none', '-u', '1000:1000', '-v', '/tmp/toilwf-08311a21086f5e9082f108730814374c/3342/job/tmpkix1u6mn:/data', '--entrypoint', '/opt/cactus/wrapper.sh', '--name', 'f4374f11-87c3-4638-873d-1c36f0785598', '--rm', 'quay.io/comparative-genomics-toolkit/cactus:v2.9.0', 'cactus_consolidated', '--seqFile', '0.6139.seqfile', '--logLevel', 'INFO', '--alignments', '0.6139_primary.paf', '--params', '0.6139.config.xml', '--outputFile', '0.6139.c2h', '--outputHalFastaFile', '0.6139.c2h.fa', '--outputReferenceFile', '0.6139.ref', '--outgroupEvents', 'Aspfov Aspnid', '--referenceEvent', '0.6139', '--threads', '22'] exited 1: