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[MainThread] [C] [toil.worker] Worker crashed with traceback: #1560

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helloworldABCD1234 opened this issue Dec 9, 2024 · 0 comments
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[2024-12-07T13:10:30+0800] [MainThread] [I] [toil-rt] cactus_consolidated(N11): Command terminated by signal 9
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Failed job accessed files:
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-RedMaskJob/instance-dxtfvekq/file-d23d99d4e0274d108fdb1a97ce6da745/test.filter.msk.remask' to path '/tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/test.fa'
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-RedMaskJob/instance-huryrfmo/file-3edb37fab00248ff92990c28c9610d99/test1.filter.msk.remask' to path '/tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/test1.fa'
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-9891u1xy/file-1d05dccfa9274441bcb53d7b4ef77448/tmpzoz9phma.tmp' to path '/tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/test2.fa'
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-9891u1xy/file-32a8dfd2a3774af68ffd094587fd5a78/tmppf5jd0dl.tmp' to path '/tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/test3.fa'
[2024-12-07T13:10:30+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-trim_unaligned_sequences/instance-9891u1xy/file-0c205db70d2748dd8e56b0de8dc52f70/tmpbi2q1q5e.tmp' to path '/tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.paf'
[2024-12-07T13:10:30+0800] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
  File "/home/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 "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2984, in _runner
    returnValues = self._run(jobGraph=None, fileStore=fileStore)
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 2895, in _run
    return self.run(fileStore)
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/toil/job.py", line 3158, in run
    rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
  File "/home/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 "/home/cactus/cactus_env/lib/python3.10/site-packages/cactus/shared/common.py", line 914, in cactus_call
    raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out))
RuntimeError: cactus_consolidated(N11): Command /usr/bin/time -f "CACTUS-LOGGED-MEMORY-IN-KB: %M" cactus_consolidated --seqFile /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.seqfile --logLevel INFO --alignments /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11_primary.paf --params /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.config.xml --outputFile /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.c2h --outputHalFastaFile /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.c2h.fa --outputReferenceFile /tmp/toilwf-f388670584325906a11528e47d7af515/2a37/job/tmp0o3s5cjs/N11.ref --outgroupEvents 'test3 test2' --referenceEvent N11 --threads 192 exited 137: 

[2024-12-07T13:10:30+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host Dell
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