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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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The cacuts operation has stopped, but there is no error message recorded in the log file. #1272

Closed panpandzf closed 10 months ago

panpandzf commented 10 months ago

As stated in the title

panpandzf commented 10 months ago

[2024-01-19T15:59:17+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/worker_log.txt [2024-01-19T15:59:17+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/worker_log.txt [2024-01-19T16:03:56+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/aa75/worker_log.txt [2024-01-19T16:03:56+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/worker_log.txt [2024-01-19T16:07:19+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:07:19.712554: Running the command: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmpwm99o5y.tmp --query --logLevel INFO" [2024-01-19T16:07:21+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:07:21.295381: Running the command: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpxmwq0q5.tmp --query --logLevel INFO" [2024-01-19T16:07:22+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:07:22.635211: Successfully ran: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmpwm99o5y.tmp --query --logLevel INFO" in 2.841 seconds with job-memory 2.0 Gi [2024-01-19T16:07:28+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:07:28.171171: Running the command: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmpb2nf0myh.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmp9unx5l6a.tmp" [2024-01-19T16:07:28+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:07:28.777413: Successfully ran: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpxmwq0q5.tmp --query --logLevel INFO" in 7.389 seconds with job-memory 2.0 Gi [2024-01-19T16:08:04+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:08:04.284976: Successfully ran: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmpb2nf0myh.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/ff3d/9a80/tmp9unx5l6a.tmp" in 36.106 seconds with job-memory 2.0 Gi [2024-01-19T16:08:04+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:08:04.965780: Running the command: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpfvu20k7n.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpipdtdgw.tmp" [2024-01-19T16:08:29+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:08:29.133259: Successfully ran: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpfvu20k7n.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/2e49/8c7d/tmpipdtdgw.tmp" in 24.1527 seconds with job-memory 2.0 Gi [2024-01-19T16:08:51+0800] [MainThread] [I] [toil.leader] 3 jobs are running, 0 jobs are issued and waiting to run [2024-01-19T16:10:56+0800] [MainThread] [I] [toil.leader] Issued job 'chain_alignments' kind-chain_alignments/instance-nvv400us v1 with job batch system ID: 9382 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False [2024-01-19T16:11:38+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:11:38.052348: Running the command: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmpqlwesorg.tmp --query --logLevel INFO" [2024-01-19T16:11:42+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:11:42.618794: Successfully ran: "paffy dechunk -i /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmpqlwesorg.tmp --query --logLevel INFO" in 4.323 seconds with job-memory 2.0 Gi [2024-01-19T16:11:47+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:11:47.844998: Running the command: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmppaw0wea2.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmpemvs9a7f.tmp" [2024-01-19T16:12:21+0800] [MainThread] [I] [toil-rt] 2024-01-19 16:12:21.311031: Successfully ran: "cat /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmppaw0wea2.tmp /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/0906/0db4/tmpemvs9a7f.tmp" in 33.4335 seconds with job-memory 2.0 Gi [2024-01-19T16:14:58+0800] [MainThread] [I] [toil.leader] Issued job 'chain_alignments' kind-chain_alignments/instance-jgwl3vce v1 with job batch system ID: 9383 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False [2024-01-19T16:19:22+0800] [MainThread] [I] [toil.leader] Issued job 'chain_one_alignment' kind-chain_one_alignment/instance-j48_xnh6 v1 with job batch system ID: 9384 and disk: 4.5 Gi, memory: 23.9 Gi, cores: 1, accelerators: [], preemptible: False [2024-01-19T16:19:22+0800] [MainThread] [I] [toil.leader] Issued job 'chain_one_alignment' kind-chain_one_alignment/instance-7jecg8tx v1 with job batch system ID: 9385 and disk: 4.4 Gi, memory: 23.4 Gi, cores: 1, accelerators: [], preemptible: False [2024-01-19T16:19:22+0800] [MainThread] [I] [toil.leader] Issued job 'chain_one_alignment' kind-chain_one_alignment/instance-orrwneq3 v1 with job batch system ID: 9386 and disk: 2.7 Gi, memory: 14.5 Gi, cores: 1, accelerators: [], preemptible: False [2024-01-19T16:28:10+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/fff4/worker_log.txt [2024-01-19T16:32:23+0800] [MainThread] [I] [toil.worker] Redirecting logging to /Path/to//workdir/7f14abdfc249547e8b8b119593839b49/896a/worker_log.txt