search

PacificBiosciences / pb-metagenomics-tools

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
BSD 3-Clause Clear License
174 stars 35 forks source link

[Error] ChechM2 Diamond database incompatible with Diamond version #58

Closed franlat closed 1 year ago

franlat commented 1 year ago

Pipeline: HiFi-MAG-Pipeline Issue: Error in Checkm2ContigAnalysis step after downloading CheckM2 database. I am assuming based on the log file that the checkm2 database diamond version does not match with the diamond version installed in the conda environment. Perhaps I can download another version of the database (or construct it myself)?

Here is the snippet from the std error: 

[Fri May 26 01:52:19 2023]
Error in rule Checkm2ContigAnalysis:
    jobid: 19
    output: /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/1-long-contigs/BL_0902/checkm2/quality_report.tsv
    log: /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/logs/BL_0902.Checkm2ContigAnalysis.log (check log file(s) for error message)
    conda-env: /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/.snakemake/conda/5d983589
    shell:
        checkm2 predict -i /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/1-long-contigs/BL_0902/bins/ -o /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/1-long-contigs/BL_0902/checkm2/ -x fa -t 12 --force --database_path /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/CheckM2_database/uniref100.KO.1.dmnd --remove_intermediates --tmpdir /home/flatorre/scratch/flatorre/tmp &> /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/logs/BL_0902.Checkm2ContigAnalysis.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

And the log file for BL_0902.Checkm2ContigAnalysis.log:

[05/26/2023 01:51:39 AM] INFO: Running CheckM2 version 1.0.1
[05/26/2023 01:51:39 AM] INFO: Custom database path provided for predict run. Checking database at /mnt/lustre/scratch/flatorre/pb-metagenomics-tools/HiFi-MAG-Pipeline/CheckM2_database/uniref100.KO.1.dmnd...
[05/26/2023 01:52:00 AM] INFO: Running quality prediction workflow with 12 threads.
[05/26/2023 01:52:02 AM] INFO: Calling genes in 13 bins with 12 threads:
^M    Finished processing 1 of 13 (7.69%) bins.^M    Finished processing 2 of 13 (15.38%) bins.^M    Finished processing 3 of 13 (23.08%) bins.^M    Finished processing 4 of 13 (30.77%) bins.^M    Finished processing 5 of 13 (38.46%) bins.^M    Finished processing 6 of 13 (46.15%) bins.^M    Finished processing 7 of 13 (53.85%) bins.^M    Finished processing 8 of 13 (61.54%) bins.^M    Finished processing 9 of 13 (69.23%) bins.^M    Finished processing 10 of 13 (76.92%) bins.^M    Finished processing 11 of 13 (84.62%) bins.^M    Finished processing 12 of 13 (92.31%) bins.^M    Finished processing 13 of 13 (100.00%) bins.
[05/26/2023 01:52:17 AM] INFO: Calculating metadata for 13 bins with 12 threads:
^M    Finished processing 1 of 13 (7.69%) bin metadata.^M    Finished processing 2 of 13 (15.38%) bin metadata.^M    Finished processing 3 of 13 (23.08%) bin metadata.^M    Finished processing 4 of 13 (30.77%) bin metadata.^M    Finished processing 5 of 13 (38.46%) bin metadata.^M    Finished processing 6 of 13 (46.15%) bin metadata.^M    Finished processing 7 of 13 (53.85%) bin metadata.^M    Finished processing 8 of 13 (61.54%) bin metadata.^M    Finished processing 9 of 13 (69.23%) bin metadata.^M    Finished processing 10 of 13 (76.92%) bin metadata.
^M    Finished processing 11 of 13 (84.62%) bin metadata.^M    Finished processing 12 of 13 (92.31%) bin metadata.^M    Finished processing 13 of 13 (100.00%) bin metadata.
[05/26/2023 01:52:18 AM] INFO: Annotating input genomes with DIAMOND using 12 threads
Error: Database was built with a different version of Diamond and is incompatible.
[05/26/2023 01:52:18 AM] ERROR: Error: DIAMOND failed to generate output.
franlat commented 1 year ago

I think I already know what happened. I think I had one of the other conda environment activated when I launched the snakemake command that messed with the diamond version and didn't allow for the correct one to be loaded.

I'm closing this because it was a mistake on my part!