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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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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

Open mahesh-panchal opened 7 months ago

mahesh-panchal commented 7 months ago

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.