minimap2 cannot works correctly in the "Running Contig Analyzer" step

[shiinachaos]

Hi,

I'm using QUAST to evaluate a metagenomic assembly (fasta).
I installe QUAST using conda and download test data.

conda install -y -c bioconda quast
quast-download-silva
wget quast.sf.net/test_data.tar.gz && tar xzf test_data.tar.gz

When I test the software in normal mode, minimap2 works correctly in the "Running Contig Analyzer" step.
The command is quast.py --test, and the output log is:

2024-01-09 18:28:35
Running Contig analyzer...
  1  contigs_1
  2  contigs_2
  1  Logging to files /mnt/HP_data/5_Sequence_analysis/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr...
  2  Logging to files /mnt/HP_data/5_Sequence_analysis/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr...
  1  Aligning contigs to the reference
  2  Aligning contigs to the reference
  2  /home/gongzc/mambaforge/envs/meta/lib/python3.10/site-packages/quast_libs/minimap2/minimap2 \
     -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
     0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 32 quast_test_output/quast_corrected_input/reference.fasta \
     quast_test_output/quast_corrected_input/contigs_2.fasta > quast_test_output/contigs_reports/minimap_output/contigs_2.coords_tmp \
     2>> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr
  1  /home/gongzc/mambaforge/envs/meta/lib/python3.10/site-packages/quast_libs/minimap2/minimap2 \
     -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
     0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 32 quast_test_output/quast_corrected_input/reference.fasta \
     quast_test_output/quast_corrected_input/contigs_1.fasta > quast_test_output/contigs_reports/minimap_output/contigs_1.coords_tmp \
     2>> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr
  1  Analysis is finished.

  2  Analysis is finished.

However, when I test the software in meta mode, minimap2 cannot works correctly in the "Running Contig Analyzer" step.
The command is metaquast.py --test-no-ref, and the output log is:

ERROR! Critical! Tried to use minimap2, but it was unavailable despite QUAST's sincere expectations! E.g., the binary file is present but corrupted.
Possible workarounds:
1. Remove the minimap2 binary and restart QUAST (it will automatically try to recompile it): rm -f <quast_installation_dir>/quast_libs/minimap2/minimap2
2. Go to <quast_installation_dir>/quast_libs/minimap2/ and recompile minimap2 manually
3. Install a proper version of minimap2 and add it to your PATH environment variable

I recompiled minimap2 based on the provided solution in the error message, but the issue still persists.
This confuses me a lot. And hope to get your help, thanks.