I recently tried starting a run of deepCSA using v1.1.0, and got the following three errors:
First, from BBGTOOLS:DEEPCSA:ONCODRIVE3D:ONCODRIVE3D_RUN:
2026-05-21 13:38:46,347 - INFO | oncodrive3d.run.clustering - Computing missense mut probabilities using mutabilities..
2026-05-21 13:38:46,352 - CRITICAL | root - Traceback (most recent call last):
File "/usr/local/bin/oncodrive3D", line 8, in <module>
sys.exit(oncodrive3D())
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/scripts/globals.py", line 46, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/scripts/main.py", line 204, in run
run_clustering(input_path,
File "/usr/local/lib/python3.10/site-packages/scripts/run/clustering.py", line 672, in run_clustering
result_gene = result_np_gene
UnboundLocalError: local variable 'result_np_gene' referenced before assignment
Second, from BBGTOOLS:DEEPCSA:ONCODRIVECLUSTL:ONCODRIVECLUSTL:
2026-05-21 13:38:50,611 [43] INFO root: Initializing OncodriveCLUSTL...
2026-05-21 13:38:50,611 [43] WARNING root:
Running with default simulating, smoothing and clustering OncodriveCLUSTL parameters. Default parameters may not be optimal for your data.
Please, read Supplementary Methods to perform model selection for your data.
2026-05-21 13:38:50,612 [43] INFO root: Computing missense mut probabilities using mutabilities...
2026-05-21 13:38:50,612 [43] WARNING root:
Signatures will be calculated as mutation frequencies: # mutated ref>alt k-mer counts / # total substitutions
Please, read Supplementary Methods to perform a more accurate signatures calculation
2026-05-21 13:38:50,612 [43] INFO root: Parsing genomic regions and mutations...
2026-05-21 13:38:50,613 [43] INFO root: Regions parsed
2026-05-21 13:38:50,614 [43] INFO root: Mutations parsed
2026-05-21 13:38:50,614 [43] INFO root: Validated elements in genomic regions: 1
2026-05-21 13:38:50,614 [43] INFO root: Validated elements with mutations: 1
2026-05-21 13:38:50,614 [43] INFO root: Total substitution mutations: 1
2026-05-21 13:38:50,616 [43] CRITICAL root: Traceback (most recent call last):
File "/usr/local/bin/oncodriveclustl", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/oncodriveclustl/main.py", line 285, in main
raise excep.UserInputError('No element found with enough mutations to perform analysis')
oncodriveclustl.utils.exceptions.UserInputError: No element found with enough mutations to perform analysis
and third, from BBGTOOLS:DEEPCSA:SIGNATURESALL:HDPEXTRACTION:RUN_HDP_CHAIN_SAMPLING:
Run citation('hdp') for citation instructions,
and file.show(system.file('LICENSE', package='hdp')) for license details.
Error in hdp_setdata(hdp_mut, dpindex = dpindex:numdp(hdp_mut), samples_input) :
dpindex must be positive integers no greater than
numdp(hdp) with no duplicates
Execution halted
(this is the entire contents of .command.log).
In the first case, this needs to be fixed. In the second case, there needs to be something in place so "not enough mutations" doesn't cause the whole step to evaluate as failed. In the third case, I'm not sure what is happening.
I recently tried starting a run of deepCSA using v1.1.0, and got the following three errors:
First, from
BBGTOOLS:DEEPCSA:ONCODRIVE3D:ONCODRIVE3D_RUN:Second, from
BBGTOOLS:DEEPCSA:ONCODRIVECLUSTL:ONCODRIVECLUSTL:and third, from
BBGTOOLS:DEEPCSA:SIGNATURESALL:HDPEXTRACTION:RUN_HDP_CHAIN_SAMPLING:(this is the entire contents of
.command.log).In the first case, this needs to be fixed. In the second case, there needs to be something in place so "not enough mutations" doesn't cause the whole step to evaluate as failed. In the third case, I'm not sure what is happening.