raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out))

[1321425744zy]

[2024-06-12T03:09:17+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-filter_paf/instance-s12rs4k7/file-4421866d3777474c84511365ecf2e950/mg.paf.filter.overlap' to path '/tmp/71b48063b6315421a2b6d3c1c1327852/c93b/a690/tmp9juo1yll/Anc0.paf' Traceback (most recent call last): File "/root/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 "/root/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2829, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/root/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2746, in _run return self.run(fileStore) File "/root/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2974, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/root/cactus/cactus_env/lib/python3.10/site-packages/cactus/pipeline/cactus_workflow.py", line 143, in cactus_cons messages = cactus_call(check_output=True, returnStdErr=True, File "/root/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(NC_052487.1): Command ['docker', 'run', '--interactive', '--net=host', '--log-driver=none', '-u', '0:0', '-v', '/tmp/71b48063b6315421a2b6d3c1c1327852/c93b/a690/tmp9juo1yll:/data', '--entrypoint', '/opt/cactus/wrapper.sh', '--name', '17f75b85-ce33-4591-846d-6d8d5f5f3125', '--rm', 'quay.io/comparative-genomics-toolkit/cactus:v2.8.2', 'cactus_consolidated', '--sequences', 'GCA002240015.2 GCA002240015.2.fa GCA002260605.1 GCA002260605.1.fa GCA002260645.1 GCA002260645.1.fa GCA002260665.1 GCA002260665.1.fa GCA002904275.2 GCA002904275.2.fa GCA2712375.1 GCA2712375.1.fa GCF730915.1 GCF730915.1.fa MINIGRAPH MINIGRAPH.fa', '--speciesTree', '(GCA002240015.2:0.025,GCA002260605.1:0.025,GCA002260645.1:0.025,GCA002260665.1:0.025,GCA002904275.2:0.025,GCA2712375.1:0.025,GCF730915.1:0.025,MINIGRAPH:0.025)Anc0;', '--logLevel', 'INFO', '--alignments', 'Anc0_primary.paf', '--params', 'Anc0.config.xml', '--outputFile', 'Anc0.c2h', '--outputHalFastaFile', 'Anc0.c2h.fa', '--outputReferenceFile', 'Anc0.ref', '--outgroupEvents', '', '--referenceEvent', 'Anc0', '--threads', '64'] exited 1: [2024-06-12T03:09:18+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host node105 <=========

[glennhickey]

There's not enough of the log here to diagnose, but it could be that it ran out of memory.