glennhickey
commented
1 month ago Are your two logs on the same data? They seem quite different, apart from the 2.8 one not crashing, the alignment stats seem quite different. Ex in 2.8
cactus_consolidated(Anc00): Sequence graph statistics after annealing: cactus_consolidated(Anc00): There were 553175 blocks in the sequence graph, representing 51022420 total aligned bases
vs 2.9
cactus_consolidated(Anc00): Sequence graph statistics after annealing: cactus_consolidated(Anc00): There were 97456 blocks in the sequence graph, representing 20691777 total aligned bases
where there aren't any changes between the versions that should have any effect. If you are able to share the input data, I can try to reproduce the crash here.
aebaci
Can Cactus be used to align the list of CDS from several species? Impliying that none of the sequences will be masked.I've tried it and I got an error (below). I thought it was a version problem, but after installing 2.9 it didn't work again. Seems to be at the hal export phase. I have attached the log from the run with cactus 2.8 and 2.9. Thanks.
log2-8.txt log2-9.txt Below is the last message from the run with 2.9 [2024-08-14T17:24:46+0100] [MainThread] [C] [toil.worker] Worker crashed with traceback: Traceback (most recent call last): File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/toil/worker.py", line 438, in workerScript job._runner(jobGraph=None, jobStore=job_store, fileStore=fileStore, defer=defer) File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/toil/job.py", line 2984, in _runner returnValues = self._run(jobGraph=None, fileStore=fileStore) File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/toil/job.py", line 2895, in _run return self.run(fileStore) File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/toil/job.py", line 3158, in run rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/cactus/progressive/cactus_progressive.py", line 268, in export_hal cactus_call(parameters=args, job_memory=job.memory) File "/home/antonella/cactus-bin-v2.9.0/venv-cactus-v2.9.0/lib/python3.10/site-packages/cactus/shared/common.py", line 912, in cactus_call raise RuntimeError("{}Command {} signaled {}: {}".format(sigill_msg, call, signal.Signals(-process.returncode).name, out)) RuntimeError: Command ['halAppendCactusSubtree', '/tmp/toilwf-0a5809edfa225b61820ea0c9e64dccad/fa00/job/tmp1c2cq32i/Anc07.hal.c2h', '/tmp/toilwf-0a5809edfa225b61820ea0c9e64dccad/fa00/job/tmp1c2cq32i/Anc07.hal.fa', '/tmp/toilwf-0a5809edfa225b61820ea0c9e64dccad/fa00/job/tmp1c2cq32i/Anc07.newick', '/tmp/toilwf-0a5809edfa225b61820ea0c9e64dccad/fa00/job/tmp1c2cq32i/Anc00.hal', '--outgroups', 'RHOEC.Rhodnius_ecuadoriensis,RHOBR.Rhodnius_brethesi'] signaled SIGABRT: stderr=terminate called after throwing an instance of 'hal_exception' what(): DnaAccess is dirty, flush() should have been called