DIAMOND errors cause entire CheckM2 run to fail

[AroneyS]

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Two of these genomes (genomes.tar.gz) fail due to DIAMOND errors for some reason. When this occurs, the entire run fails. I have only seen this with CheckM2 v1.1.0.

checkm2 predict -t 16 \
    -i genomes -x fna \
    -o checkm2_all_genomes
# [11/04/2025 02:08:11 PM] INFO: Running CheckM2 version 1.1.0
# [11/04/2025 02:08:11 PM] INFO: Running quality prediction workflow with 16 threads.
# [11/04/2025 02:08:11 PM] INFO: Calling genes in 3 bins with 16 threads:

#     Finished processing 1 of 3 (33.33%) bins.
#     Finished processing 2 of 3 (66.67%) bins.free(): invalid pointer

#     Finished processing 3 of 3 (100.00%) bins.
# [11/04/2025 02:09:57 PM] INFO: Calculating metadata for 3 bins with 16 threads:

#     Finished processing 1 of 3 (33.33%) bin metadata.
#     Finished processing 2 of 3 (66.67%) bin metadata.
#     Finished processing 3 of 3 (100.00%) bin metadata.
# [11/04/2025 02:09:58 PM] INFO: Annotating input genomes with DIAMOND using 16 threads
# Error: Missing fields in input line
# [11/04/2025 02:11:32 PM] ERROR: An error occured while running DIAMOND: Command 'diamond blastp --outfmt 6 --max-target-seqs 1 --query /tmp/pbs.13909777.aqua/tmpcogwjftw -o checkm2_all_genomes/diamond_output/DIAMOND_RESULTS.tsv --threads 16 --db /work/microbiome/db/CheckM2_database/uniref100.KO.1.dmnd --query-cover 80 --subject-cover 80 --id 30 --evalue 1e-05 --block-size 2.0 --tmpdir /tmp/pbs.13909777.aqua/tmp1_5ijliq --quiet ' returned non-zero exit status 1.


# Run just genomes/metabat_spec_bins.tsv.007_sub.fna
checkm2 predict -t 16 \
    -i genomes/metabat_spec_bins.tsv.007_sub.fna \
    -o checkm2_metabat_spec_bins_007
# [11/04/2025 08:26:32 PM] INFO: Running CheckM2 version 1.1.0
# [11/04/2025 08:26:32 PM] INFO: Running quality prediction workflow with 16 threads.
# [11/04/2025 08:26:32 PM] INFO: Calling genes in 1 bins with 16 threads:

#     Finished processing 1 of 1 (100.00%) bins.
# [11/04/2025 08:26:36 PM] INFO: Calculating metadata for 1 bins with 16 threads:

#     Finished processing 1 of 1 (100.00%) bin metadata.
# [11/04/2025 08:26:36 PM] INFO: Annotating input genomes with DIAMOND using 16 threads
# [11/04/2025 08:26:50 PM] INFO: Processing DIAMOND output
# [11/04/2025 08:26:51 PM] INFO: Predicting completeness and contamination using ML models.
# [11/04/2025 08:26:53 PM] INFO: Parsing all results and constructing final output table.
# [11/04/2025 08:26:53 PM] INFO: CheckM2 finished successfully.


# Run just genomes/metabat_spec_bins.tsv.011.fna
checkm2 predict -t 16 \
    -i genomes/metabat_spec_bins.tsv.011.fna \
    -o checkm2_metabat_spec_bins_011
# [11/04/2025 08:27:25 PM] INFO: Running CheckM2 version 1.1.0
# [11/04/2025 08:27:25 PM] INFO: Running quality prediction workflow with 16 threads.
# [11/04/2025 08:27:25 PM] INFO: Calling genes in 1 bins with 16 threads:
# free(): invalid pointer

#     Finished processing 1 of 1 (100.00%) bins.
# [11/04/2025 08:28:47 PM] INFO: Calculating metadata for 1 bins with 16 threads:

#     Finished processing 1 of 1 (100.00%) bin metadata.
# [11/04/2025 08:28:47 PM] INFO: Annotating input genomes with DIAMOND using 16 threads
# Error: Missing fields in input line
# [11/04/2025 08:28:47 PM] ERROR: An error occured while running DIAMOND: Command 'diamond blastp --outfmt 6 --max-target-seqs 1 --query /tmp/pbs.13920842.aqua/tmpv4ctf2fn -o checkm2_metabat_spec_bins_011/diamond_output/DIAMOND_RESULTS.tsv --threads 16 --db /work/microbiome/db/CheckM2_database/uniref100.KO.1.dmnd --query-cover 80 --subject-cover 80 --id 30 --evalue 1e-05 --block-size 2.0 --tmpdir /tmp/pbs.13920842.aqua/tmp5946ky2p --quiet ' returned non-zero exit status 1.


# Run just genomes/semibin_refined_bins.tsv.115_sub.fna
checkm2 predict -t 16 \
    -i genomes/semibin_refined_bins.tsv.115_sub.fna \
    -o checkm2_semibin_refined_bins_115_sub
# [11/04/2025 08:28:33 PM] INFO: Running CheckM2 version 1.1.0
# [11/04/2025 08:28:33 PM] INFO: Running quality prediction workflow with 16 threads.
# [11/04/2025 08:28:33 PM] INFO: Calling genes in 1 bins with 16 threads:

#     Finished processing 1 of 1 (100.00%) bins.
# [11/04/2025 08:28:35 PM] INFO: Calculating metadata for 1 bins with 16 threads:

#     Finished processing 1 of 1 (100.00%) bin metadata.
# [11/04/2025 08:28:35 PM] INFO: Annotating input genomes with DIAMOND using 16 threads
# [11/04/2025 08:28:51 PM] INFO: Processing DIAMOND output
# [11/04/2025 08:28:51 PM] ERROR: No DIAMOND annotation was generated. Exiting