Hello,
I am trying to run Megalodon, but it is giving different results and errors with different numbers of threads.
When I run it with the default thread setting.
It produced mapping results
and giving these warnings and errors
[00:18:51] Running Megalodon version 2.5.0
******************** WARNING: "mods" output requested, so "per_read_mods" will be added to outputs. ********************
[00:18:51] Loading guppy basecalling backend
******************** WARNING [00:18:54.992:MainProcess:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [00:18:54.993:MainProcess:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
[00:18:55] Loading reference
******************** WARNING [00:19:29.566:MainProcess:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [00:19:29.566:MainProcess:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
[00:19:29] Loaded Remora model calls modified bases: m=5mC (alt to C)
[00:19:29] Modified base motifs derived from Remora model. Ignoring --mod-motif.
[00:19:34] Preparing workers to process reads
[00:19:35] Processing reads
Full output or empty input queues indicate I/O bottleneck
3 most common unsuccessful processing stages:
----- ******************** WARNING [00:19:35.923:ReadWorker000:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [00:19:35.923:ReadWorker000:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ******************** 0%| | 0/10000
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
45.2% ( 136 reads) : No alignment /home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/site-packages/megalodon/mods.py:1368: RuntimeWarning: invalid value encountered in cast
33.6% ( 247 reads) : No alignment
26.4% ( 194 reads) : Guppy server timeout (see --guppy-timeout argument)
0.5% ( 4 reads) : Unexpected error
Read Processing: 100%|██████████| 800/800 [1:43:17<00:00, 7.75s/reads, samples/s=8.6e+3]
input queue capacity extract_signal : 0%| | 0/10000
output queue capacity basecalls : 0%| | 0/10000
output queue capacity per_read_mods : 0%| | 0/10000
******************** WARNING: Unexpected errors occured. See full error stack traces for first (up to) 50 errors in "unexpected_megalodon_errors.8938.err" ********************
[02:02:53] Unsuccessful processing types:
34.0% ( 272 reads) : No alignment
24.2% ( 194 reads) : Guppy server timeout (see --guppy-timeout argument)
0.5% ( 4 reads) : Unexpected error
[02:02:53] Waiting for mods database to complete indexing
[02:03:06] Spawning modified base aggregation processes
[02:03:06] Aggregating 12939 per-read modified base statistics
[02:03:06] NOTE: If this step is very slow, ensure the output directory is located on a fast read disk (e.g. local SSD). Aggregation can be restarted using the `megalodon_extras aggregate run` command
Mods: 2%|▏ | 200/12939 [00:00<00:11, 1092.94 per-read calls/s]Process Process-10:
AttributeError: 'NoneType' object has no attribute 'exp'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/site-packages/megalodon/aggregate.py", line 143, in _agg_mods_worker
mod_site = agg_mods.compute_mod_stats(
File "/home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/site-packages/megalodon/mods.py", line 3034, in compute_mod_stats
mod_props, valid_cov = self.est_binary_thresh(mod_type_stats)
File "/home/ashutosh/anaconda3/envs/MEGALODON/lib/python3.9/site-packages/megalodon/mods.py", line 2872, in est_binary_thresh
can_lp = np.log1p(-np.exp(mt_lps).sum())
TypeError: loop of ufunc does not support argument 0 of type NoneType which has no callable exp method
Mods: 2%|▏ | 200/12939 [00:00<00:40, 316.19 per-read calls/s]
[02:03:08] Mega Done
When I run it with 40 threads.
It produced mapping results
and giving these warnings but not produced error as above (AttributeError: 'NoneType' object has no attribute 'exp')
[11:45:42] Running Megalodon version 2.5.0
******************** WARNING: "mods" output requested, so "per_read_mods" will be added to outputs. ********************
[11:45:42] Loading guppy basecalling backend
******************** WARNING [11:45:53.983:MainProcess:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:45:53.984:MainProcess:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
[11:45:54] Loading reference
******************** WARNING [11:46:28.408:MainProcess:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:28.408:MainProcess:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
[11:46:28] Loaded Remora model calls modified bases: m=5mC (alt to C)
[11:46:28] Modified base motifs derived from Remora model. Ignoring --mod-motif.
[11:46:33] Preparing workers to process reads
[11:46:33] Processing reads
Full output or empty input queues indicate I/O bottleneck
3 most common unsuccessful processing stages:
----- ******************** WARNING [11:46:33.908:ReadWorker000:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:33.908:ReadWorker000:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ******************** 0%| | 0/10000
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.000:ReadWorker001:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.001:ReadWorker001:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.079:ReadWorker002:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.079:ReadWorker002:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.212:ReadWorker003:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.212:ReadWorker003:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.339:ReadWorker004:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.340:ReadWorker004:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.434:ReadWorker005:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.435:ReadWorker005:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.570:ReadWorker006:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.570:ReadWorker006:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.679:ReadWorker007:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.679:ReadWorker007:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.751:ReadWorker008:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.751:ReadWorker008:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.862:ReadWorker009:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.862:ReadWorker009:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:34.983:ReadWorker010:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:34.984:ReadWorker010:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.080:ReadWorker011:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.080:ReadWorker011:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.183:ReadWorker012:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.183:ReadWorker012:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.289:ReadWorker013:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.289:ReadWorker013:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.369:ReadWorker014:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.369:ReadWorker014:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.496:ReadWorker015:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.496:ReadWorker015:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.591:ReadWorker016:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.591:ReadWorker016:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.707:ReadWorker017:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.707:ReadWorker017:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.826:ReadWorker018:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.826:ReadWorker018:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:35.924:ReadWorker019:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:35.924:ReadWorker019:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.029:ReadWorker020:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.029:ReadWorker020:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.106:ReadWorker021:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.106:ReadWorker021:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.219:ReadWorker022:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.219:ReadWorker022:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.306:ReadWorker023:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.306:ReadWorker023:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.400:ReadWorker024:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.400:ReadWorker024:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.507:ReadWorker025:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.507:ReadWorker025:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.608:ReadWorker026:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.608:ReadWorker026:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.761:ReadWorker027:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.762:ReadWorker027:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.868:ReadWorker028:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.868:ReadWorker028:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:36.947:ReadWorker029:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:36.947:ReadWorker029:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.083:ReadWorker030:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.083:ReadWorker030:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.156:ReadWorker031:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.156:ReadWorker031:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.248:ReadWorker032:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.248:ReadWorker032:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.352:ReadWorker033:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.352:ReadWorker033:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.438:ReadWorker034:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.438:ReadWorker034:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.519:ReadWorker035:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.520:ReadWorker035:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.596:ReadWorker036:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.596:ReadWorker036:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.718:ReadWorker037:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.718:ReadWorker037:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.799:ReadWorker038:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.799:ReadWorker038:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING [11:46:37.872:ReadWorker039:MainThread:model_util.py:350]: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING: reverse signal attribute not found in model. Assuming False ********************
******************** WARNING [11:46:37.872:ReadWorker039:MainThread:model_util.py:355]: Centered picoamp scaling attribute not found in model. Assuming None ********************
******************** WARNING: Centered picoamp scaling attribute not found in model. Assuming None ********************
96.0% ( 704 reads) : Guppy server timeout (see --guppy-timeout argument)
2.2% ( 16 reads) : No alignment
0.1% ( 1 reads) : Unexpected error
Read Processing: 100%|██████████| 800/800 [04:04<00:00, 3.27reads/s, samples/s=2.22e+5]
input queue capacity extract_signal : 0%| | 0/10000
output queue capacity basecalls : 0%| | 0/10000
output queue capacity per_read_mods : 0%| | 0/10000
******************** WARNING: Unexpected errors occured. See full error stack traces for first (up to) 50 errors in "unexpected_megalodon_errors.6543.err" ********************
[11:50:38] Unsuccessful processing types:
96.4% ( 771 reads) : Guppy server timeout (see --guppy-timeout argument)
2.0% ( 16 reads) : No alignment
0.1% ( 1 reads) : Unexpected error
[11:50:38] Waiting for mods database to complete indexing
[11:50:39] Spawning modified base aggregation processes
[11:50:43] Aggregating 460 per-read modified base statistics
[11:50:43] NOTE: If this step is very slow, ensure the output directory is located on a fast read disk (e.g. local SSD). Aggregation can be restarted using the `megalodon_extras aggregate run` command
Mods: 100%|██████████| 460/460 [00:01<00:00, 371.45 per-read calls/s]
[11:50:45] Mega Done
Any suggestion,
Thanks,
Harshad
Hello,
I am trying to run Megalodon, but it is giving different results and errors with different numbers of threads.
When I run it with the default thread setting.
It produced mapping results
and giving these warnings and errors
When I run it with 40 threads.
It produced mapping results
and giving these warnings but not produced error as above (AttributeError: 'NoneType' object has no attribute 'exp')
Any suggestion,
Thanks,
Harshad