-
Notifications
You must be signed in to change notification settings - Fork 76
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Function not implemented: '/usr/local/lib/python3.10/site-packages/quast_libs/gridss' #235
Comments
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 |
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'
The text was updated successfully, but these errors were encountered: