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Busco doesn't exit with an error when one of the subtools is killed, or print a suitable error message #85

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mahesh-panchal opened this issue Mar 1, 2024 · 0 comments

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Describe the bug

Metaeuk in Busco was likely killed due to using up too much memory, but Busco did not detect it and just reported Metaeuk found no genes.

2024-02-26 13:56:18 INFO:       ***** Start a BUSCO v5.5.0 analysis, current time: 02/26/2024 13:56:18 *****
2024-02-26 13:56:18 INFO:       Configuring BUSCO with local environment
2024-02-26 13:56:18 INFO:       Mode is genome
2024-02-26 13:56:18 INFO:       Downloading information on latest versions of BUSCO data...
2024-02-26 13:56:21 INFO:       Running in batch mode. 1 input files found in /scratch/45246902/nxf.KDjoMEs3BQ/input_seqs
2024-02-26 13:56:21 INFO:       Input file is /scratch/45246902/nxf.KDjoMEs3BQ/input_seqs/hifiasm-raw-default.asm.bp.p_ctg.fasta
2024-02-26 13:56:21 INFO:       Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2024-01-08.tar.gz'
2024-02-26 13:56:23 INFO:       Decompressing file '/scratch/45246902/nxf.KDjoMEs3BQ/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2024-02-26 13:57:16 INFO:       Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2024-01-08)
2024-02-26 13:57:16 INFO:       Running 1 job(s) on bbtools, starting at 02/26/2024 13:57:16
2024-02-26 13:58:17 INFO:       [bbtools]       1 of 1 task(s) completed
2024-02-26 13:58:18 INFO:       Running 1 job(s) on metaeuk, starting at 02/26/2024 13:58:18
2024-02-26 14:34:45 INFO:       [metaeuk]       1 of 1 task(s) completed
2024-02-26 14:34:49 ERROR:      Metaeuk did not recognize any genes matching the dataset arthropoda_odb10 in the input file. If this is unexpected, check your input file and your installation of Metaeuk

mv: cannot stat 'hifiasm-raw-default-arthropoda_odb10-busco/*/short_summary.*.json': No such file or directory
mv: cannot stat 'hifiasm-raw-default-arthropoda_odb10-busco/*/short_summary.*.txt': No such file or directory
Short summaries were not available: No genes were found.

To Reproduce
Steps to reproduce the behavior:

  1. Run busco without enough memory and let slurm kill Metaeuk for using too much memory.

Expected behavior

My expectation was that Busco would detect Metaeuk had not finished correctly.

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