[Errno 2] No such file or directory: '$HOME/.quast/blast'

[marcinschmidt]

I am running metaQuast inside singularity container, but Quast looks for a database which it downloaded itself in $HOME/.quast/blast.
How can I make Quast to download its database to specific location (question 1) and use it frome there, and in following analyses show Quast where the database is already (question 2)?

my .log file:

/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/EGG-INFO/scripts/metaquast.py ERR6229432.megahit.out.final.contigs.fa ERR6229432.complex.megahit.out.final.contigs.fa ERR6229432.metaSPAdes.out.final.contigs.fa ERR6229432.metaSPAdes.out.final.scaffolds.fa -l MegaHit_std,MegaHit_complex,metaSPAdes_contigs,metaSPAdes_scaffolds -t 40 --silent

Version: 5.3.0, fb88221c

System information:
  OS: Linux-5.14.0-427.28.1.el9_4.x86_64-x86_64-with-glibc2.35 (linux_64)
  Python version: 3.10.12
  CPUs number: 112

Started: 2025-05-21 16:42:14

Logging to /jobdir/quast_results/results_2025_05_21_16_42_13/metaquast.log

Contigs:
  Pre-processing...
  1  ERR6229432.megahit.out.final.contigs.fa ==> MegaHit_std
  2  ERR6229432.complex.megahit.out.final.contigs.fa ==> MegaHit_complex
  3  ERR6229432.metaSPAdes.out.final.contigs.fa ==> metaSPAdes_contigs
  4  ERR6229432.metaSPAdes.out.final.scaffolds.fa ==> metaSPAdes_scaffolds

No references are provided, starting to search for reference genomes in SILVA 16S rRNA database and to download them from NCBI...

2025-05-21 16:42:26

[Errno 2] No such file or directory: '/mnt/storage_3/home/mschmidt/.quast/blast'
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/EGG-INFO/scripts/metaquast.py", line 428, in <module>
    return_code = main(sys.argv[1:])
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/EGG-INFO/scripts/metaquast.py", line 201, in main
    ref_fpaths = search_references_meta.do(assemblies, labels, downloaded_dirpath, corrected_dirpath, qconfig.references_txt)
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/quast_libs/search_references_meta.py", line 373, in do
    species_scores, species_by_assembly, replacement_dict = process_blast(blast_assemblies, downloaded_dirpath,
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/quast_libs/search_references_meta.py", line 430, in process_blast
    if not download_blast_binaries(filenames=blast_filenames):
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/quast_libs/qutils.py", line 998, in download_blast_binaries
    blast_dirpath = get_dir_for_download('blast', 'BLAST', filenames, logger, only_clean=only_clean)
  File "/usr/local/lib/python3.10/dist-packages/quast-5.3.0-py3.10.egg/quast_libs/qutils.py", line 961, in get_dir_for_download
    os.makedirs(tool_dirpath)
  File "/usr/lib/python3.10/os.py", line 225, in makedirs
    mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/storage_3/home/mschmidt/.quast/blast'