sokrypton / sokrypton/ColabFold
Failed to mmap memory dataSize
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Description
I've been using colabfold_search smoothly for a long time. Then all of a sudden the below error came.
Versions:
colabfold 1.6.1 pypi_0 pypi
mmseqs2 18.8cc5c hd6d6fdc_0 bioconda
Here is the log:
INFO:colabfold.mmseqs.search:Running mmseqs createdb msas_spy_af3/query.fas msas_spy_af3/qdb --shuffle 0 --dbtype 1
msas_spy_af3/qdb exists and will be overwritten
createdb msas_spy_af3/query.fas msas_spy_af3/qdb --shuffle 0 --dbtype 1
Converting sequences
[
Time for merging to qdb_h: 0h 0m 0s 57ms
Time for merging to qdb: 0h 0m 0s 71ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 196ms
INFO:colabfold.mmseqs.search:Running mmseqs search msas_spy_af3/qdb .../local/ColabFold/dbs/uniref30_2302_db msas_spy_af3/res msas_spy_af3/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
Failed to mmap memory dataSize=244437757952 File=.../local/ColabFold/dbs/uniref30_2302_db.idx. Error 12.
Traceback (most recent call last):
File ".../miniconda3/envs/cf/bin/colabfold_search", line 6, in <module>
sys.exit(main())
~~~~^^
File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 481, in main
mmseqs_search_monomer(
~~~~~~~~~~~~~~~~~~~~~^
mmseqs=args.mmseqs,
^^^^^^^^^^^^^^^^^^^
...<19 lines>...
unpack=args.unpack,
^^^^^^^^^^^^^^^^^^^
)
^
File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 131, in mmseqs_search_monomer
run_mmseqs(mmseqs, ["search", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("tmp"), "--threads", str(threads)] + search_param)
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 47, in run_mmseqs
subprocess.check_call([mmseqs] + params)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File ".../miniconda3/envs/cf/lib/python3.13/subprocess.py", line 419, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'search', PosixPath('msas_spy_af3/qdb'), PosixPath('.../local/ColabFold/dbs/uniref30_2302_db'), PosixPath('msas_spy_af3/res'), PosixPath('msas_spy_af3/tmp'), '--threads', '64', '--num-iterations', '3', '--db-load-mode', '0', '-a', '-e', '0.1', '--max-seqs', '10000', '--gpu', '1', '--prefilter-mode', '1']' returned non-zero exit status 1.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading colabfold/mmseqs/search.py, especially mmseqs_search_monomer and run_mmseqs, then reproduce the logged mmseqs search command using the stated versions and database path. Done means determining why the uniref30_2302_db search fails to mmap and making the same search complete or documenting the confirmed environmental limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100