makeblastdb died with a Signals.SIGBUS: 7 error

[taffners]

Hello,

I'm getting a Signals:SIGBUS: 7 error. I'm not sure why this is happening. Kleborate was previously running without issue for years.

$ python3 --version Python 3.7.12 $ python3 -c "import Bio; print(Bio.version)" 1.79 $ blastn -version blastn: 2.12.0+ Package: blast 2.12.0, build Jul 13 2021 09:03:00 $ mash --version 2.3 $ python /data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate-runner.py --version Kleborate v2.1.0

Here's the traceback:

python /data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate-runner.py -k -r -a /data1/Samantha_Test/micro_data/2024_06_24/BWH_1999_K_pne_2024_06_24/BWH_1999_K_pne_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2001_E_clo_2024_06_24/BWH_2001_E_clo_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2002_K_pne_2024_06_24/BWH_2002_K_pne_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2004_K_pne_2024_06_24/BWH_2004_K_pne_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2008_K_aer_2024_06_24/BWH_2008_K_aer_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2011_K_pne_2024_06_24/BWH_2011_K_pne_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2012_E_clo_2024_06_24/BWH_2012_E_clo_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_2014_K_aer_2024_06_24/BWH_2014_K_aer_2024_06_24_contigs.fasta /data1/Samantha_Test/micro_data/2024_06_24/BWH_9_K_pne_2024_06_24/BWH_9_K_pne_2024_06_24_contigs.fasta > /data1/micro_results/step_1/2024_06_24_summarize_step1/Kleborate_results.tsv

Traceback (most recent call last):
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate-runner.py", line 22, in <module>
    main()
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/__main__.py", line 61, in main
    results.update(get_all_virulence_results(data_folder, contigs, args))
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/__main__.py", line 479, in get_all_virulence_results
    get_iuc_mlst_results(data_folder, contigs, args),
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/__main__.py", line 518, in get_iuc_mlst_results
    'iuc unknown', 3, get_iuc_mlst_header, args)
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/__main__.py", line 465, in get_virulence_cluster_results
    min_spurious_ident=args.min_spurious_identity)
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/mlstBLAST.py", line 46, in mlst_blast
    hits = run_blastn(seqs, contigs, min_spurious_cov, min_spurious_ident)
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/blastn.py", line 22, in run_blastn
    build_blast_database_if_needed(db)
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/blastn.py", line 139, in build_blast_database_if_needed
    shell=True)
  File "/data1/Samantha_Test/micro_pipeline/local_software_installs/miniconda3/envs/micro_pipeline_3_7/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'makeblastdb -dbtype nucl -in /data1/Samantha_Test/micro_pipeline/local_software_installs/Kleborate/kleborate/data/iuc_alleles.fasta' died with <Signals.SIGBUS: 7>.