IndexError: list index out of range
I submitted an array job to my cluster to run BUSCO on 239 genomes. However, seven of them failed. In the log file, it's written:
.... (log file truncated)....
2024-03-27 11:51:53 ERROR:busco.BuscoRunner list index out of range
2024-03-27 11:51:53 DEBUG:busco.BuscoRunner list index out of range
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/busco/BuscoRunner.py", line 165, in run
self.runner.run_analysis()
File "/usr/local/lib/python3.7/site-packages/busco/BuscoRunner.py", line 564, in run_analysis
self.analysis.run_analysis()
File "/usr/local/lib/python3.7/site-packages/busco/analysis/GenomeAnalysis.py", line 866, in run_analysis
busco_ids=incomplete_buscos,
File "/usr/local/lib/python3.7/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/busco/analysis/BuscoAnalysis.py", line 136, in run_hmmer
self.validate_output()
File "/usr/local/lib/python3.7/site-packages/busco/analysis/GenomeAnalysis.py", line 195, in validate_output
overlaps, exon_records, hmmer_results
File "/usr/local/lib/python3.7/site-packages/busco/analysis/GenomeAnalysis.py", line 427, in handle_overlaps
overlap_entry, exon_records, hmmer_results
File "/usr/local/lib/python3.7/site-packages/busco/analysis/GenomeAnalysis.py", line 467, in handle_diff_busco_overlap
if hmmer_match_details1[0]["score"] > hmmer_match_details2[0]["score"]:
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/busco/run_BUSCO.py", line 74, in run
runner.run()
File "/usr/local/lib/python3.7/site-packages/busco/BuscoLogger.py", line 62, in wrapped_func
self.retval = func(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/busco/BuscoRunner.py", line 197, in run
raise BatchFatalError(str(exc_value))
busco.Exceptions.BatchFatalError: list index out of range
2024-03-27 11:51:53 ERROR:busco.BuscoRunner BUSCO analysis failed!
2024-03-27 11:51:53 ERROR:busco.BuscoRunner Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues
2024-03-27 11:51:54 DEBUG:urllib3.connectionpool Starting new HTTPS connection (1): busco-data.ezlab.org:443
2024-03-27 11:51:54 DEBUG:urllib3.connectionpool Starting new HTTPS connection (1): busco-data.ezlab.org:443
2024-03-27 11:51:54 DEBUG:urllib3.connectionpool https://busco-data.ezlab.org:443 "PUT /upload/rundata202403271151543254974.txt HTTP/1.1" 201 0
2024-03-27 11:51:54 DEBUG:urllib3.connectionpool https://busco-data.ezlab.org:443 "PUT /upload/rundata202403271151543254974.txt HTTP/1.1" 201 0
2024-03-27 11:51:54 DEBUG:busco.run_BUSCO File uploaded successfully.
It seems like the BUSCO run was successful but it didn't produce the busco sequences. I ran this job using parameters as follow, with BUSCO v 5.7.0:
busco -i dataset/${REFGEN}/${REFGEN}_genomic.fna -m genome -l endopterygota_odb10 -c 20 -f -o dataset/${REFGEN}/${REFGEN} --download_path busco_downloads --metaeuk &> busco_${REFGEN}.log
Could you help me figure out the issue and how to solve it? Many thanks!
Edited by Arif Maulana