Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.
Hi,
I got an error when when running ananse network (v0.5.1) for non-model organisms.
ananse network -n 1 Cni_G_binding/binding.h5 -e G.mean.tpm -o Cni_G.ANANSE_network.tsv -g Cni.v2.assembly.chr.fasta -a Cni.v2.longest.gene.bed --include-promoter --include-enhancer
I have tried many times to running with different thread counts such as 1, 4, 12, 48, but they resulted in the same error as follows:
`2024-07-18 19:08:50 | INFO | Loading expression data
2024-07-18 19:08:50 | INFO | 100% of TFs found in both BED and expression file(s)
2024-07-18 19:08:51 | DEBUG | Loading tf binding activity data
2024-07-18 19:08:51 | INFO | Loading binding data
2024-07-18 19:08:51 | INFO | Using all 268 TFs.
2024-07-18 19:08:51 | INFO | Using all 184688 regions.
Aggregating: 0%| | 0/20 [00:00<?, ?contig/s]
Aggregating on Chr4. Overall progress: 0%| | 0/20 [00:00<?, ?contig/s]
Aggregating on Chr4. Overall progress: 5%|▌ | 1/20 [00:07<02:15, 7.15s/contig]
Aggregating on Chr2. Overall progress: 5%|▌ | 1/20 [00:07<02:15, 7.15s/contig]
Aggregating on Chr2. Overall progress: 10%|█ | 2/20 [00:13<01:56, 6.49s/contig]
Aggregating on Chr10. Overall progress: 10%|█ | 2/20 [00:13<01:56, 6.49s/contig]
Aggregating on Chr10. Overall progress: 15%|█▌ | 3/20 [00:18<01:39, 5.84s/contig]
Aggregating on Chr6. Overall progress: 15%|█▌ | 3/20 [00:18<01:39, 5.84s/contig]
Aggregating on Chr6. Overall progress: 20%|██ | 4/20 [00:24<01:38, 6.14s/contig]
Aggregating on fragScaff_342. Overall progress: 20%|██ | 4/20 [00:24<01:38, 6.14s/contig]
Aggregating on fragScaff_342. Overall progress: 25%|██▌ | 5/20 [00:28<01:17, 5.19s/contig]
Aggregating on fragScaff_111. Overall progress: 25%|██▌ | 5/20 [00:28<01:17, 5.19s/contig]
Aggregating on fragScaff_111. Overall progress: 30%|███ | 6/20 [00:31<01:03, 4.57s/contig]
Aggregating on Chr1. Overall progress: 30%|███ | 6/20 [00:31<01:03, 4.57s/contig]
Aggregating on Chr1. Overall progress: 35%|███▌ | 7/20 [00:38<01:08, 5.31s/contig]
Aggregating on fragScaff_9. Overall progress: 35%|███▌ | 7/20 [00:38<01:08, 5.31s/contig]
Aggregating on fragScaff_9. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig]
Aggregating on fragScaff_67. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig]2024-07-18 19:09:33 | DEBUG | No genes found on fragScaff_67
Aggregating on fragScaff_314. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig]
Aggregating on fragScaff_314. Overall progress: 50%|█████ | 10/20 [00:45<00:32, 3.22s/contig]
Aggregating on Chr8. Overall progress: 50%|█████ | 10/20 [00:45<00:32, 3.22s/contig]
Aggregating on Chr8. Overall progress: 55%|█████▌ | 11/20 [00:49<00:32, 3.61s/contig]
Aggregating on Chr7. Overall progress: 55%|█████▌ | 11/20 [00:49<00:32, 3.61s/contig]
Aggregating on Chr7. Overall progress: 60%|██████ | 12/20 [00:55<00:33, 4.17s/contig]
Aggregating on fragScaff_50. Overall progress: 60%|██████ | 12/20 [00:55<00:33, 4.17s/contig]
Aggregating on fragScaff_50. Overall progress: 65%|██████▌ | 13/20 [00:58<00:27, 3.90s/contig]
Aggregating on Chr5. Overall progress: 65%|██████▌ | 13/20 [00:58<00:27, 3.90s/contig]
Aggregating on Chr5. Overall progress: 70%|███████ | 14/20 [01:05<00:27, 4.62s/contig]
Aggregating on fragScaff_356. Overall progress: 70%|███████ | 14/20 [01:05<00:27, 4.62s/contig]
Aggregating on fragScaff_356. Overall progress: 75%|███████▌ | 15/20 [01:08<00:21, 4.24s/contig]
Aggregating on fragScaff_6. Overall progress: 75%|███████▌ | 15/20 [01:08<00:21, 4.24s/contig]
Aggregating on fragScaff_6. Overall progress: 80%|████████ | 16/20 [01:11<00:15, 3.95s/contig]
Aggregating on fragScaff_1. Overall progress: 80%|████████ | 16/20 [01:11<00:15, 3.95s/contig]
Aggregating on fragScaff_1. Overall progress: 85%|████████▌ | 17/20 [01:14<00:11, 3.73s/contig]
Aggregating on fragScaff_15. Overall progress: 85%|████████▌ | 17/20 [01:14<00:11, 3.73s/contig]
Aggregating on fragScaff_15. Overall progress: 90%|█████████ | 18/20 [01:18<00:07, 3.58s/contig]
Aggregating on Chr9. Overall progress: 90%|█████████ | 18/20 [01:18<00:07, 3.58s/contig]
Aggregating on Chr9. Overall progress: 95%|█████████▌| 19/20 [01:23<00:04, 4.19s/contig]
Aggregating on Chr3. Overall progress: 95%|█████████▌| 19/20 [01:23<00:04, 4.19s/contig]
Aggregating on Chr3. Overall progress: 100%|██████████| 20/20 [01:30<00:00, 4.99s/contig]
Aggregating on Chr3. Overall progress: 100%|██████████| 20/20 [01:30<00:00, 4.53s/contig]
2024-07-18 19:10:41,093 - distributed.core - ERROR - Exception while handling op shuffle_receive
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,572 - distributed.core - ERROR - Exception while handling op shuffle_receive
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(self.args, self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,585 - distributed.shuffle._comms - ERROR -
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process
await self.send(address, shards)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send
return await self.rpc(address).shuffle_receive(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(self.args, self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,619 - distributed.shuffle._comms - ERROR -
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process
await self.send(address, shards)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send
return await self.rpc(address).shuffle_receive(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, *kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(self.args, **self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,699 - distributed.worker - WARNING - Compute Failed
Key: ('shuffle-transfer-88e0cfaa8489bdcfe8c2e364a0dbb424', 12)
Function: shuffle_transfer
args: ( tf_target weighted_binding _partitions
0 CNI_011695—CNI_029437 0.009343 8
1 CNI_028301—CNI_029437 0.008639 18
2 CNI_003268—CNI_029437 0.010407 3
3 CNI_007104—CNI_029437 0.004793 5
4 CNI_017922—CNI_029437 0.006409 12
.. ... ... ...
263 CNI_017527—CNI_029437 0.009470 12
264 CNI_008075—CNI_029437 0.011968 5
265 CNI_008091—CNI_029437 0.004803 5
266 CNI_025698—CNI_029437 0.005376 17
267 CNI_018002—CNI_029437 0.008188 13
2024-07-18 19:10:41,708 - distributed.core - ERROR - Exception while handling op shuffle_receive
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive
shuffle = await self._get_shuffle_run(shuffle_id, run_id)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 709, in _get_shuffle_run
raise shuffle._exception
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer
return _get_worker_extension().add_partition(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition
shuffle = self.get_or_create_shuffle(shuffle_id, type=type, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle
return sync(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f
result = yield future
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run
value = future.result()
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle
raise shuffle._exception
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,737 - distributed.shuffle._comms - ERROR -
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process
await self.send(address, shards)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send
return await self.rpc(address).shuffle_receive(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive
shuffle = await self._get_shuffle_run(shuffle_id, run_id)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 709, in _get_shuffle_run
raise shuffle._exception
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer
return _get_worker_extension().add_partition(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition
shuffle = self.get_or_create_shuffle(shuffle_id, type=type, *kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle
return sync(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f
result = yield future
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run
value = future.result()
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle
raise shuffle._exception
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(self.args, self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
AssertionError
2024-07-18 19:10:41,753 - distributed.core - ERROR - Exception while handling op shuffle_get
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm
result = handler(**msg)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get
state = self.states[id]
KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424'
2024-07-18 19:10:41 | ERROR | An error has been caught in function '', process 'MainProcess' (1953258), thread 'MainThread' (22995272511808):
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer
return _get_worker_extension().add_partition(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition
shuffle = self.get_or_create_shuffle(shuffle_id, type=type, *kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle
return sync(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f
result = yield future
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run
value = future.result()
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle
raise shuffle._exception
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive
await shuffle.receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive
await self._receive(data)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive
groups = await self.offload(self._repartition_buffers, filtered)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload
return await asyncio.get_running_loop().run_in_executor(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(self.args, **self.kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers
groups = split_by_partition(table, self.column)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition
assert len(partitions) == len(shards)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/bin/ananse", line 609, in
args.func(args)
│ │ └ Namespace(binding='Cni_G_binding/binding.h5', fin_expression=['G.mean.tpm'], genome='Cni.v2.assembly.chr.fasta', annotation='...
│ └ <function network at 0x14e8e01f8550>
└ Namespace(binding='Cni_G_binding/binding.h5', fin_expression=['G.mean.tpm'], genome='Cni.v2.assembly.chr.fasta', annotation='...
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/ananse/commands/network.py", line 37, in network
b.run_network(
│ └ <function Network.run_network at 0x14e9d3d4a550>
└ <ananse.network.Network object at 0x14e8c7a50550>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/ananse/network.py", line 619, in run_network
df_binding = self.aggregate_binding(
│ └ <function Network.aggregate_binding at 0x14e9d3d4a3a0>
└ <ananse.network.Network object at 0x14e8c7a50550>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/ananse/network.py", line 465, in aggregate_binding
df = ddf.compute()
│ └ <function DaskMethodsMixin.compute at 0x14e9fc7ac700>
└ Dask DataFrame Structure:
weighted_binding
npartitions=19
CNI_000236—CNI_000017...
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/dask/base.py", line 310, in compute
(result,) = compute(self, traverse=False, kwargs)
│ │ └ {}
│ └ Dask DataFrame Structure:
│ weighted_binding
│ npartitions=19
│ CNI_000236—CNI_000017...
└ <function compute at 0x14e9fc7acb80>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/dask/base.py", line 595, in compute
results = schedule(dsk, keys, kwargs)
│ │ │ └ {}
│ │ └ [[('sort_index-db7e01245a05884dd414652652916111', 0), ('sort_index-db7e01245a05884dd414652652916111', 1), ('sort_index-db7e01...
│ └ HighLevelGraph with 3 layers.
│ <dask.highlevelgraph.HighLevelGraph object at 0x14e5ddc3b040>
│ 0. assign-3f2c55f95675be1e0c4e6a...
└ <bound method Client.get of <Client: 'tcp://127.0.0.1:40061' processes=1 threads=2, memory=0.98 TiB>>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/client.py", line 3243, in get
results = self.gather(packed, asynchronous=asynchronous, direct=direct)
│ │ │ │ └ None
│ │ │ └ None
│ │ └ [[<Future: cancelled, key: ('sort_index-db7e01245a05884dd414652652916111', 0)>, <Future: cancelled, key: ('sort_index-db7e012...
│ └ <function Client.gather at 0x14e8c7b83c10>
└ <Client: 'tcp://127.0.0.1:40061' processes=1 threads=2, memory=0.98 TiB>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/client.py", line 2368, in gather
return self.sync(
│ └ <function SyncMethodMixin.sync at 0x14e8d7fbd3a0>
└ <Client: 'tcp://127.0.0.1:40061' processes=1 threads=2, memory=0.98 TiB>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 351, in sync
return sync(
└ <function sync at 0x14e8d7fbd430>
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync
raise exc.with_traceback(tb)
│ │ └ <traceback object at 0x14e8b762ad40>
│ └ <method 'with_traceback' of 'BaseException' objects>
└ RuntimeError('shuffle_transfer failed during shuffle 88e0cfaa8489bdcfe8c2e364a0dbb424')
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f
result = yield future
└ <Task finished name='Task-14748' coro=<Client._gather() done, defined at /gpfshddpool/home/.conda/envs/ananse/lib/p...
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run
value = future.result()
└ None
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/client.py", line 2231, in _gather
raise exception.with_traceback(traceback)
│ │ └ <traceback object at 0x14e84dd39e40>
│ └ <method 'with_traceback' of 'BaseException' objects>
└ RuntimeError('shuffle_transfer failed during shuffle 88e0cfaa8489bdcfe8c2e364a0dbb424')
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 73, in shuffle_transfer
raise RuntimeError(f"shuffle_transfer failed during shuffle {id}") from e
RuntimeError: shuffle_transfer failed during shuffle 88e0cfaa8489bdcfe8c2e364a0dbb424
2024-07-18 19:10:42,071 - distributed.core - ERROR - Exception while handling op shuffle_receive
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive
shuffle = await self._get_shuffle_run(shuffle_id, run_id)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 699, in _get_shuffle_run
shuffle = await self._refresh_shuffle(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 766, in _refresh_shuffle
result = await self.worker.scheduler.shuffle_get(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm
result = handler(msg)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get
state = self.states[id]
KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424'
2024-07-18 19:10:42,080 - distributed.shuffle._comms - ERROR - '88e0cfaa8489bdcfe8c2e364a0dbb424'
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process
await self.send(address, shards)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send
return await self.rpc(address).shuffle_receive(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm
result = await result
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive
shuffle = await self._get_shuffle_run(shuffle_id, run_id)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 699, in _get_shuffle_run
shuffle = await self._refresh_shuffle(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 766, in _refresh_shuffle
result = await self.worker.scheduler.shuffle_get(
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc
return await send_recv(comm=comm, op=key, kwargs)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv
raise exc.with_traceback(tb)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm
result = handler(**msg)
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get
state = self.states[id]
KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424'
`
What should I do to resolve the problem?
Hi, I got an error when when running ananse network (v0.5.1) for non-model organisms.
ananse network -n 1 Cni_G_binding/binding.h5 -e G.mean.tpm -o Cni_G.ANANSE_network.tsv -g Cni.v2.assembly.chr.fasta -a Cni.v2.longest.gene.bed --include-promoter --include-enhancerI have tried many times to running with different thread counts such as 1, 4, 12, 48, but they resulted in the same error as follows: `2024-07-18 19:08:50 | INFO | Loading expression data 2024-07-18 19:08:50 | INFO | 100% of TFs found in both BED and expression file(s) 2024-07-18 19:08:51 | DEBUG | Loading tf binding activity data 2024-07-18 19:08:51 | INFO | Loading binding data 2024-07-18 19:08:51 | INFO | Using all 268 TFs. 2024-07-18 19:08:51 | INFO | Using all 184688 regions.
Aggregating: 0%| | 0/20 [00:00<?, ?contig/s] Aggregating on Chr4. Overall progress: 0%| | 0/20 [00:00<?, ?contig/s] Aggregating on Chr4. Overall progress: 5%|▌ | 1/20 [00:07<02:15, 7.15s/contig] Aggregating on Chr2. Overall progress: 5%|▌ | 1/20 [00:07<02:15, 7.15s/contig] Aggregating on Chr2. Overall progress: 10%|█ | 2/20 [00:13<01:56, 6.49s/contig] Aggregating on Chr10. Overall progress: 10%|█ | 2/20 [00:13<01:56, 6.49s/contig] Aggregating on Chr10. Overall progress: 15%|█▌ | 3/20 [00:18<01:39, 5.84s/contig] Aggregating on Chr6. Overall progress: 15%|█▌ | 3/20 [00:18<01:39, 5.84s/contig] Aggregating on Chr6. Overall progress: 20%|██ | 4/20 [00:24<01:38, 6.14s/contig] Aggregating on fragScaff_342. Overall progress: 20%|██ | 4/20 [00:24<01:38, 6.14s/contig] Aggregating on fragScaff_342. Overall progress: 25%|██▌ | 5/20 [00:28<01:17, 5.19s/contig] Aggregating on fragScaff_111. Overall progress: 25%|██▌ | 5/20 [00:28<01:17, 5.19s/contig] Aggregating on fragScaff_111. Overall progress: 30%|███ | 6/20 [00:31<01:03, 4.57s/contig] Aggregating on Chr1. Overall progress: 30%|███ | 6/20 [00:31<01:03, 4.57s/contig]
Aggregating on Chr1. Overall progress: 35%|███▌ | 7/20 [00:38<01:08, 5.31s/contig] Aggregating on fragScaff_9. Overall progress: 35%|███▌ | 7/20 [00:38<01:08, 5.31s/contig] Aggregating on fragScaff_9. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig] Aggregating on fragScaff_67. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig]2024-07-18 19:09:33 | DEBUG | No genes found on fragScaff_67
Aggregating on fragScaff_314. Overall progress: 40%|████ | 8/20 [00:41<00:55, 4.66s/contig] Aggregating on fragScaff_314. Overall progress: 50%|█████ | 10/20 [00:45<00:32, 3.22s/contig] Aggregating on Chr8. Overall progress: 50%|█████ | 10/20 [00:45<00:32, 3.22s/contig]
Aggregating on Chr8. Overall progress: 55%|█████▌ | 11/20 [00:49<00:32, 3.61s/contig] Aggregating on Chr7. Overall progress: 55%|█████▌ | 11/20 [00:49<00:32, 3.61s/contig] Aggregating on Chr7. Overall progress: 60%|██████ | 12/20 [00:55<00:33, 4.17s/contig] Aggregating on fragScaff_50. Overall progress: 60%|██████ | 12/20 [00:55<00:33, 4.17s/contig] Aggregating on fragScaff_50. Overall progress: 65%|██████▌ | 13/20 [00:58<00:27, 3.90s/contig] Aggregating on Chr5. Overall progress: 65%|██████▌ | 13/20 [00:58<00:27, 3.90s/contig]
Aggregating on Chr5. Overall progress: 70%|███████ | 14/20 [01:05<00:27, 4.62s/contig] Aggregating on fragScaff_356. Overall progress: 70%|███████ | 14/20 [01:05<00:27, 4.62s/contig] Aggregating on fragScaff_356. Overall progress: 75%|███████▌ | 15/20 [01:08<00:21, 4.24s/contig] Aggregating on fragScaff_6. Overall progress: 75%|███████▌ | 15/20 [01:08<00:21, 4.24s/contig]
Aggregating on fragScaff_6. Overall progress: 80%|████████ | 16/20 [01:11<00:15, 3.95s/contig] Aggregating on fragScaff_1. Overall progress: 80%|████████ | 16/20 [01:11<00:15, 3.95s/contig] Aggregating on fragScaff_1. Overall progress: 85%|████████▌ | 17/20 [01:14<00:11, 3.73s/contig] Aggregating on fragScaff_15. Overall progress: 85%|████████▌ | 17/20 [01:14<00:11, 3.73s/contig] Aggregating on fragScaff_15. Overall progress: 90%|█████████ | 18/20 [01:18<00:07, 3.58s/contig] Aggregating on Chr9. Overall progress: 90%|█████████ | 18/20 [01:18<00:07, 3.58s/contig]
Aggregating on Chr9. Overall progress: 95%|█████████▌| 19/20 [01:23<00:04, 4.19s/contig] Aggregating on Chr3. Overall progress: 95%|█████████▌| 19/20 [01:23<00:04, 4.19s/contig] Aggregating on Chr3. Overall progress: 100%|██████████| 20/20 [01:30<00:00, 4.99s/contig] Aggregating on Chr3. Overall progress: 100%|██████████| 20/20 [01:30<00:00, 4.53s/contig] 2024-07-18 19:10:41,093 - distributed.core - ERROR - Exception while handling op shuffle_receive Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,572 - distributed.core - ERROR - Exception while handling op shuffle_receive Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(self.args, self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,585 - distributed.shuffle._comms - ERROR - Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process await self.send(address, shards) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send return await self.rpc(address).shuffle_receive( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(self.args, self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,619 - distributed.shuffle._comms - ERROR - Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process await self.send(address, shards) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send return await self.rpc(address).shuffle_receive( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, *kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(self.args, **self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,699 - distributed.worker - WARNING - Compute Failed Key: ('shuffle-transfer-88e0cfaa8489bdcfe8c2e364a0dbb424', 12) Function: shuffle_transfer args: ( tf_target weighted_binding _partitions 0 CNI_011695—CNI_029437 0.009343 8 1 CNI_028301—CNI_029437 0.008639 18 2 CNI_003268—CNI_029437 0.010407 3 3 CNI_007104—CNI_029437 0.004793 5 4 CNI_017922—CNI_029437 0.006409 12 .. ... ... ... 263 CNI_017527—CNI_029437 0.009470 12 264 CNI_008075—CNI_029437 0.011968 5 265 CNI_008091—CNI_029437 0.004803 5 266 CNI_025698—CNI_029437 0.005376 17 267 CNI_018002—CNI_029437 0.008188 13
[268 rows x 3 columns], '88e0cfaa8489bdcfe8c2e364a0dbb424', 12, 19, '_partitions', {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}) kwargs: {} Exception: "RuntimeError('shuffle_transfer failed during shuffle 88e0cfaa8489bdcfe8c2e364a0dbb424')"
2024-07-18 19:10:41,708 - distributed.core - ERROR - Exception while handling op shuffle_receive Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive shuffle = await self._get_shuffle_run(shuffle_id, run_id) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 709, in _get_shuffle_run raise shuffle._exception File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer return _get_worker_extension().add_partition( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition shuffle = self.get_or_create_shuffle(shuffle_id, type=type, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle return sync( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f result = yield future File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run value = future.result() File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle raise shuffle._exception File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,737 - distributed.shuffle._comms - ERROR - Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process await self.send(address, shards) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send return await self.rpc(address).shuffle_receive( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive shuffle = await self._get_shuffle_run(shuffle_id, run_id) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 709, in _get_shuffle_run raise shuffle._exception File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer return _get_worker_extension().add_partition( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition shuffle = self.get_or_create_shuffle(shuffle_id, type=type, *kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle return sync( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f result = yield future File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run value = future.result() File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle raise shuffle._exception File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(self.args, self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards) AssertionError 2024-07-18 19:10:41,753 - distributed.core - ERROR - Exception while handling op shuffle_get Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm result = handler(**msg) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get state = self.states[id] KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424' 2024-07-18 19:10:41 | ERROR | An error has been caught in function '', process 'MainProcess' (1953258), thread 'MainThread' (22995272511808):
Traceback (most recent call last):
File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_shuffle.py", line 63, in shuffle_transfer return _get_worker_extension().add_partition( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 652, in add_partition shuffle = self.get_or_create_shuffle(shuffle_id, type=type, *kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 898, in get_or_create_shuffle return sync( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 418, in sync raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/utils.py", line 391, in f result = yield future File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/tornado/gen.py", line 766, in run value = future.result() File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 740, in _get_or_create_shuffle raise shuffle._exception File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 611, in shuffle_receive await shuffle.receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 486, in receive await self._receive(data) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 501, in _receive groups = await self.offload(self._repartition_buffers, filtered) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 133, in offload return await asyncio.get_running_loop().run_in_executor( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(self.args, **self.kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 510, in _repartition_buffers groups = split_by_partition(table, self.column) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 995, in split_by_partition assert len(partitions) == len(shards)
AssertionError: assert len(partitions) == len(shards)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
RuntimeError: shuffle_transfer failed during shuffle 88e0cfaa8489bdcfe8c2e364a0dbb424 2024-07-18 19:10:42,071 - distributed.core - ERROR - Exception while handling op shuffle_receive Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive shuffle = await self._get_shuffle_run(shuffle_id, run_id) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 699, in _get_shuffle_run shuffle = await self._refresh_shuffle( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 766, in _refresh_shuffle result = await self.worker.scheduler.shuffle_get( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm result = handler(msg) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get state = self.states[id] KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424' 2024-07-18 19:10:42,080 - distributed.shuffle._comms - ERROR - '88e0cfaa8489bdcfe8c2e364a0dbb424' Traceback (most recent call last): File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_comms.py", line 72, in _process await self.send(address, shards) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 124, in send return await self.rpc(address).shuffle_receive( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 924, in _handle_comm result = await result File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 610, in shuffle_receive shuffle = await self._get_shuffle_run(shuffle_id, run_id) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 699, in _get_shuffle_run shuffle = await self._refresh_shuffle( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_worker_extension.py", line 766, in _refresh_shuffle result = await self.worker.scheduler.shuffle_get( File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1365, in send_recv_from_rpc return await send_recv(comm=comm, op=key, kwargs) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 1149, in send_recv raise exc.with_traceback(tb) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/core.py", line 922, in _handle_comm result = handler(**msg) File "/gpfshddpool/home/.conda/envs/ananse/lib/python3.9/site-packages/distributed/shuffle/_scheduler_extension.py", line 143, in get state = self.states[id] KeyError: '88e0cfaa8489bdcfe8c2e364a0dbb424' ` What should I do to resolve the problem?
Thanks in advance and all the best