Function not implemented: '/usr/local/lib/python3.10/site-packages/quast_libs/gridss'

[zpagomez]

I am running quast Version: 5.2.0
but I get this error: Function not implemented: '/usr/local/lib/python3.10/site-packages/quast_libs/gridss'

This is my quast.log file
/usr/local/bin/quast.py //depot/mycospace/data/pgomezza/sphaerellopsis//6assembly_spades_firstRound/scaffolds.fasta --threads 20 --split-scaffolds --output-dir /depot/mycospace/data/pgomezza/sphaerellopsis//7quast_spades_firstAssembly --fungus --gene-finding --conserved-genes-finding --est-ref-size 26418069 --pe1 /depot/mycospace/data/pgomezza/sphaerellopsis//4reads_after_contaminants/Sphaerellopsis_cleaned_afterContaminants.1.fq --pe2 /depot/mycospace/data/pgomezza/sphaerellopsis//4reads_after_contaminants/Sphaerellopsis_cleaned_afterContaminants.2.fq

Version: 5.2.0

System information:
OS: Linux-4.18.0-372.32.1.el8_6.x86_64-x86_64-with-glibc2.28 (linux_64)
Python version: 3.10.5
CPUs number: 128

Started: 2023-02-06 14:49:22

Logging to /depot/mycospace/data/pgomezza/sphaerellopsis/7quast_spades_firstAssembly/quast.log

CWD: /depot/mycospace/data/pgomezza/sphaerellopsis/7quast_spades_firstAssembly
Main parameters:
MODE: default, threads: 20, eukaryotic: true, split scaffolds: true, min contig length: 500,
min alignment length: 65, min alignment IDY: 95.0, ambiguity: one, min local misassembly length: 200,
min extensive misassembly length: 1000

Contigs:
Pre-processing...
//depot/mycospace/data/pgomezza/sphaerellopsis//6assembly_spades_firstRound/scaffolds.fasta ==> scaffolds
breaking scaffolds into contigs:
1059 scaffolds (scaffolds) were broken into 1092 contigs (scaffolds_broken)

2023-02-06 14:49:24
Running Reads analyzer...

[Errno 38] Function not implemented: '/usr/local/lib/python3.10/site-packages/quast_libs/gridss'
Traceback (most recent call last):
File "/usr/local/bin/quast.py", line 309, in
return_code = main(sys.argv[1:])
File "/usr/local/bin/quast.py", line 118, in main
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths,
File "/usr/local/lib/python3.10/site-packages/quast_libs/reads_analyzer.py", line 934, in do
download_gridss(logger, qconfig.bed)
File "/usr/local/lib/python3.10/site-packages/quast_libs/ra_utils/misc.py", line 96, in download_gridss
gridss_dirpath = get_dir_for_download('gridss', 'GRIDSS', [gridss_fname], logger, only_clean=only_clean)
File "/usr/local/lib/python3.10/site-packages/quast_libs/qutils.py", line 960, in get_dir_for_download
os.makedirs(tool_dirpath)
File "/usr/local/lib/python3.10/os.py", line 225, in makedirs
mkdir(name, mode)
OSError: [Errno 38] Function not implemented: '/usr/local/lib/python3.10/site-packages/quast_libs/gridss'

[natefoo]

We are seeing this in Galaxy as well, although in our case, Quast runs inside of a Singularity container, and the contents are read-only (despite this we still receive errno 38), same traceback:

Traceback (most recent call last):
  File "/usr/local/bin/quast", line 309, in <module>
    return_code = main(sys.argv[1:])
  File "/usr/local/bin/quast", line 118, in main
    bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths,
  File "/usr/local/opt/quast-5.2.0/quast_libs/reads_analyzer.py", line 934, in do
    download_gridss(logger, qconfig.bed)
  File "/usr/local/opt/quast-5.2.0/quast_libs/ra_utils/misc.py", line 96, in download_gridss
    gridss_dirpath = get_dir_for_download('gridss', 'GRIDSS', [gridss_fname], logger, only_clean=only_clean)
  File "/usr/local/opt/quast-5.2.0/quast_libs/qutils.py", line 960, in get_dir_for_download
    os.makedirs(tool_dirpath)
  File "/usr/local/lib/python3.9/os.py", line 225, in makedirs
    mkdir(name, mode)
OSError: [Errno 38] Function not implemented: '/usr/local/lib/python3.9/site-packages/quast_libs/gridss'

In the case of a container install such as this, if we precreated the dir, would that be enough? Passing --no-sv (which we probably should start doing anyway) does not suppress the error, although from digging into the code a bit, it looks like it should prevent any attempt to download as long as the dir exists?