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Why can't install funannotate2 Databases#78

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@zut0may0
zut0may0
opened on Jul 15, 2026

(funannotate2) [shagan@ln01 FUNANNOTATE2_DB]$ funannotate2 install -d all
[Jul 15 11:24 AM] Python v3.10.20; funannotate2 v26.6.21; gfftk v26.5.22; buscolite v26.6.21; annorefine v2026.2.22
Traceback (most recent call last):
File "/public/home/shagan_lab/shagan/miniconda3/envs/funannotate2/bin/funannotate2", line 10, in
sys.exit(main())
File "/public/home/shagan_lab/shagan/miniconda3/envs/funannotate2/lib/python3.10/site-packages/funannotate2/main.py", line 22, in main
install(args)
File "/public/home/shagan_lab/shagan/miniconda3/envs/funannotate2/lib/python3.10/site-packages/funannotate2/install.py", line 47, in install
os.makedirs(env["FUNANNOTATE2_DB"])
File "/public/home/shagan_lab/shagan/miniconda3/envs/funannotate2/lib/python3.10/os.py", line 210, in makedirs
head, tail = path.split(name)
File "/public/home/shagan_lab/shagan/miniconda3/envs/funannotate2/lib/python3.10/posixpath.py", line 103, in split
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not bool

Activity

  1. hyphaltip commented on Jul 15, 2026

    @hyphaltip
    hyphaltip
    on Jul 15, 2026
    Collaborator

    did you set the FUNANNOTATE2_DB to a path you want to store the databases in? eg

    export FUNANNOTATE2_DB=/public/home/shagan_lab/shagan/funannotate2_db
funannotate2 install -d all

    some related instructions on setting the variable persistently in the conda env funannotate2 https://github.com/nextgenusfs/funannotate2#apple-silicon-m-series

  2. zut0may0 commented on Jul 16, 2026

    @zut0may0
    zut0may0
    on Jul 16, 2026
    Author

    yes, I did it，thanks！！But i have a new question

    funannotate2 install -d all
[Jul 15 04:00 PM] Python v3.10.20; funannotate2 v26.6.21; gfftk v26.5.22; buscolite v26.6.21; annorefine v2026.2.22
[Jul 15 04:00 PM] The backend database location is from the $FUNANNOTATE2_DB env variable: /data1/NFS/home/rdr422123/funannotate2_db
[Jul 15 04:00 PM] Retrieving download links from GitHub Repo
[Jul 15 04:00 PM] {
  "uniprot": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
  "uniprot-release": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/reldate.txt",
  "merops": "https://ftp.ebi.ac.uk/pub/databases/merops/current_release/meropsscan.lib",
  "dbCAN": "https://dbcan.s3.us-west-2.amazonaws.com/db_v5-2-9_5-5-2026/dbCAN.hmm",
  "dbCAN-tsv": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN-fam-HMMs.txt",
  "dbCAN-log": "https://raw.githubusercontent.com/nextgenusfs/funannotate2/main/funannotate2/resources/dbCAN.changelog.txt",
  "pfam": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz",
  "pfam-tsv": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz",
  "pfam-log": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam.version.gz",
  "repeats": "https://osf.io/vp87c/download?version=1",
  "go": "https://purl.obolibrary.org/obo/go.obo",
  "mibig": "https://dl.secondarymetabolites.org/mibig/mibig_prot_seqs_3.1.fasta",
  "interpro": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz",
  "interpro-tsv": "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list",
  "gene2product": "https://raw.githubusercontent.com/nextgenusfs/gene2product/master/ncbi_cleaned_gene_products.txt",
  "mito": "https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/mitochondrion.1.1.genomic.fna.gz",
  "mito-release": "https://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER"
}
[Jul 15 04:00 PM] Downloading Merops database
[Jul 15 04:01 PM] Building diamond database: diamond makedb --in merops.formatted.fa --db merops
diamond v2.2.4.184 (C) Max Planck Society for the Advancement of Science, Benjamin J. Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 80
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: merops.formatted.fa
Opening the database file...  [0.001s]
Loading sequences...  [0.014s]
Masking sequences...  [0.326s]
Writing sequences...  [0.002s]
Hashing sequences...  [0s]
Loading sequences...  [0.001s]
Writing trailer...  [0s]
Closing the input file...  [0s]
Closing the database file...  [0.003s]

Database sequences  5098
  Database letters  1303674
     Database hash  eec5a2ca499df0169c0de588711f6134
        Total time  0.351000s
[Jul 15 04:01 PM] Downloading UniProtKB/Swiss-Prot database
HTTPS download attempt 1 failed: ('Connection broken: IncompleteRead(14855691 bytes read, 78850778 more expected)', IncompleteRead(14855691 bytes read, 78850778 more expected)). Retrying in 5 seconds...
[Jul 15 05:31 PM] Building diamond database: diamond makedb --in uniprot_sprot.fasta --db uniprot
diamond v2.2.4.184 (C) Max Planck Society for the Advancement of Science, Benjamin J. Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 80
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: uniprot_sprot.fasta
Opening the database file...  [0.054s]
Loading sequences...  [1.375s]
Masking sequences...  [17.036s]
Writing sequences...  [0.388s]
Hashing sequences...  [0.118s]
Loading sequences...  [0.002s]
Writing trailer...  [0.094s]
Closing the input file...  [0s]
Closing the database file...  [3.823s]

Database sequences  575503
  Database letters  208906902
     Database hash  13235b1a95ab6064d49e5d251937b926
        Total time  22.895000s
[Jul 15 05:31 PM] Downloading dbCAN database
[Jul 15 06:45 PM] Copied dbCAN metadata files from package resources
[Jul 15 06:45 PM] Creating dbCAN HMM database and pressing with pyhmmer
[Jul 15 06:45 PM] Downloading Pfam database
HTTPS download attempt 1 failed: ('Connection broken: IncompleteRead(3343689 bytes read, 414816825 more expected)', IncompleteRead(3343689 bytes read, 414816825 more expected)). Retrying in 5 seconds...
HTTPS download attempt 2 failed: HTTPSConnectionPool(host='ftp.ebi.ac.uk', port=443): Read timed out.. Retrying in 5 seconds...
HTTPS download failed after 3 attempts: ('Connection broken: IncompleteRead(783689 bytes read, 417376825 more expected)', IncompleteRead(783689 bytes read, 417376825 more expected))
Trying FTP fallback for https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
FTP download failed: <urlopen error timed out>
Traceback (most recent call last):
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 905, in _error_catcher
    yield
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 1043, in _raw_read
    raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
urllib3.exceptions.IncompleteRead: IncompleteRead(783689 bytes read, 417376825 more expected)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/requests/models.py", line 937, in generate
    yield from self.raw.stream(chunk_size, decode_content=True)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 1267, in stream
    data = self.read(amt=amt, decode_content=decode_content)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 1155, in read
    data = self._raw_read(amt)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 1021, in _raw_read
    with self._error_catcher():
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/contextlib.py", line 153, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/urllib3/response.py", line 925, in _error_catcher
    raise ProtocolError(arg, e) from e
urllib3.exceptions.ProtocolError: ('Connection broken: IncompleteRead(783689 bytes read, 417376825 more expected)', IncompleteRead(783689 bytes read, 417376825 more expected))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/funannotate2/utilities.py", line 249, in download
    for chunk in r.iter_content(chunk_size=8192):
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/requests/models.py", line 939, in generate
    raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ('Connection broken: IncompleteRead(783689 bytes read, 417376825 more expected)', IncompleteRead(783689 bytes read, 417376825 more expected))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/bin/funannotate2", line 10, in <module>
    sys.exit(main())
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/funannotate2/__main__.py", line 22, in main
    install(args)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/funannotate2/install.py", line 228, in install
    data = pfamDB(wget=args.wget)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/funannotate2/install.py", line 589, in pfamDB
    download(DBURL.get("pfam"), hmm + ".gz", wget=wget)
  File "/data1/NFS/home/rdr422123/anaconda3/envs/funannotate2_env/lib/python3.10/site-packages/funannotate2/utilities.py", line 273, in download
    raise Exception(f"Download failed: {str(e)}")
Exception: Download failed: ('Connection broken: IncompleteRead(783689 bytes read, 417376825 more expected)', IncompleteRead(783689 bytes read, 417376825 more expected))

    did i need Installing Databases one by one ?

  3. zut0may0 commented on Jul 16, 2026

    @zut0may0
    zut0may0
    on Jul 16, 2026
    Author

    @hyphaltip I need use VPN to install ?

  4. nextgenusfs commented on Jul 16, 2026

    @nextgenusfs
    nextgenusfs
    on Jul 16, 2026
    Owner

    Looks like your internet connection is quite slow and unstable. I'll try to push a fix that might improve this, no guarantees it will work though.

  5. nextgenusfs commented on Jul 16, 2026

    @nextgenusfs
    nextgenusfs
    on Jul 16, 2026
    Owner

    Try to install from latest, ie from your environment run this:

    python -m pip install git+https://github.com/nextgenusfs/funannotate2.git --upgrade --force --no-deps

    And then try the install command again and see if it's able to complete.

  6. peterjc commented on Aug 4, 2026

    @peterjc
    peterjc
    on Aug 4, 2026
    Contributor

    I filed a duplicate of the original issue about an exception error when $FUNANNOTATE2_DB isn't set as #83 (whoops), but my fix in #84 has been merged.

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