CRITICAL:busco.BuscoRunner Unhandled exception ocurred.
Hi there!
I'm currently running BUSCO on a genome of approximately 900Mbp with two different datasets (insecta_odb10 and hemiptera_odb10) independently on a LSF grid. I got a different error message for each database, which didn't help when looking for a solution. Here are the error lines of both busco.log
files:
- This one is for the run with
insecta_odb10
:
/2024-03-11 14:30:41 CRITICAL:busco.BuscoRunner Unhandled exception occurred:
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 188, in run
self.runner.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 564, in run_analysis
self.analysis.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 859, in run_analysis
self.run_hmmer(
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/BuscoAnalysis.py", line 136, in run_hmmer
self.validate_output()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 190, in validate_output
exon_records = self.get_exon_records(hmmer_results)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 227, in get_exon_records
matched_records[gene_id] = self.gene_details[details[0]["ref gene ID"]]
KeyError: '104526at50557_13249_0:000c8e|scf7180000041612:F:-5696:scf7180000039292:F:-2904:scf7180000032916:R:26'
2024-03-11 14:30:41 ERROR:busco.BuscoRunner '104526at50557_13249_0:000c8e|scf7180000041612:F:-5696:scf7180000039292:F:-2904:scf7180000032916:R:26'
2024-03-11 14:30:41 DEBUG:busco.BuscoRunner '104526at50557_13249_0:000c8e|scf7180000041612:F:-5696:scf7180000039292:F:-2904:scf7180000032916:R:26'
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 188, in run
self.runner.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 564, in run_analysis
self.analysis.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 859, in run_analysis
self.run_hmmer(
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/BuscoAnalysis.py", line 136, in run_hmmer
self.validate_output()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 190, in validate_output
exon_records = self.get_exon_records(hmmer_results)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 227, in get_exon_records
matched_records[gene_id] = self.gene_details[details[0]["ref gene ID"]]
KeyError: '104526at50557_13249_0:000c8e|scf7180000041612:F:-5696:scf7180000039292:F:-2904:scf7180000032916:R:26'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/run_BUSCO.py", line 73, in run
runner.run()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 223, in run
raise BatchFatalError(str(exc_value))
busco.Exceptions.BatchFatalError: '104526at50557_13249_0:000c8e|scf7180000041612:F:-5696:scf7180000039292:F:-2904:scf7180000032916:R:26'
2024-03-11 14:30:41 ERROR:busco.BuscoRunner BUSCO analysis failed!
2024-03-11 14:30:41 ERROR:busco.BuscoRunner
- The following is for the run with
hemiptera_odb10
:
2024-03-11 14:22:55 INFO:busco.busco_tools.Toolset [hmmsearch] 2510 of 2510 task(s) completed
2024-03-11 14:23:00 CRITICAL:busco.BuscoRunner Unhandled exception occurred:
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 188, in run
self.runner.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 564, in run_analysis
self.analysis.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 859, in run_analysis
self.run_hmmer(
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/BuscoAnalysis.py", line 135, in run_hmmer
self.hmmer_runner.process_output()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 537, in process_output
results = self.load_results_from_file(filename)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 604, in load_results_from_file
matched_record = self.parse_hmmer_output(filename, busco_query)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 362, in parse_hmmer_output
if self._check_overlap(matched_genes, gene_id):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 407, in _check_overlap
start1, end1 = coords1.split(
ValueError: not enough values to unpack (expected 2, got 1)
2024-03-11 14:23:00 ERROR:busco.BuscoRunner not enough values to unpack (expected 2, got 1)
2024-03-11 14:23:00 DEBUG:busco.BuscoRunner not enough values to unpack (expected 2, got 1)
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 188, in run
self.runner.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 564, in run_analysis
self.analysis.run_analysis()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/GenomeAnalysis.py", line 859, in run_analysis
self.run_hmmer(
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/analysis/BuscoAnalysis.py", line 135, in run_hmmer
self.hmmer_runner.process_output()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 537, in process_output
results = self.load_results_from_file(filename)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 604, in load_results_from_file
matched_record = self.parse_hmmer_output(filename, busco_query)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 362, in parse_hmmer_output
if self._check_overlap(matched_genes, gene_id):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/busco_tools/hmmer.py", line 407, in _check_overlap
start1, end1 = coords1.split(
ValueError: not enough values to unpack (expected 2, got 1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/run_BUSCO.py", line 73, in run
runner.run()
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/sc/arion/projects/MML/conda/envs/QA_tools/lib/python3.9/site-packages/busco/BuscoRunner.py", line 223, in run
raise BatchFatalError(str(exc_value))
busco.Exceptions.BatchFatalError: not enough values to unpack (expected 2, got 1)
2024-03-11 14:23:00 ERROR:busco.BuscoRunner BUSCO analysis failed!
2024-03-11 14:23:00 ERROR:busco.BuscoRunner
I'm not sure if this will be of any help, but the genome was assembled with masurca and scaffolded with SAMBA, which are included in the same toolkit.
Appreciate any help with this issue :)