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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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plantismash #769

Open zhangwenda0518 opened 2 years ago

zhangwenda0518 commented 2 years ago

Dear author I'm using funannotate remote to run annotation plantismash, but an error occurred. Could you give me some suggestions?

Thanks very much！！！

Details are as follows

Are you using the latest release?

funannotate check --show-versions

1.8.13

Describe the bug [Aug 23 10:41 AM]: OS: CentOS Linux 8, 256 cores, ~ 660 GB RAM. Python: 3.6.15 [Aug 23 10:41 AM]: Running 1.8.13 [Aug 23 10:41 AM]: Output directory functional_annotation already exists [Aug 23 10:41 AM]: Checking GenBank file for annotation Traceback (most recent call last): File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connectionpool.py", line 710, in urlopen chunked=chunked, File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connectionpool.py", line 386, in _make_request self._validate_conn(conn) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connectionpool.py", line 1040, in _validate_conn conn.connect() File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connection.py", line 467, in connect _match_hostname(cert, self.assert_hostname or server_hostname) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connection.py", line 540, in _match_hostname match_hostname(cert, asserted_hostname) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/util/ssl_match_hostname.py", line 155, in match_hostname raise CertificateError("hostname %r doesn't match %r" % (hostname, dnsnames[0])) urllib3.util.ssl_match_hostname.CertificateError: hostname 'plantismash.secondarymetabolites.org' doesn't match '*.bioinformatics.nl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/adapters.py", line 450, in send timeout=timeout File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/connectionpool.py", line 786, in urlopen method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/urllib3/util/retry.py", line 592, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='plantismash.secondarymetabolites.org', port=443): Max retries exceeded with url: /api/v1.0/version (Caused by SSLError(CertificateError("hostname 'plantismash.secondarymetabolites.org' doesn't match '*.bioinformatics.nl'",),))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/bin/funannotate", line 8, in sys.exit(main()) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate/remote.py", line 242, in main version = requests.get(base_address+"/api/v1.0/version") File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/api.py", line 75, in get return request('get', url, params=params, kwargs) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/sessions.py", line 529, in request resp = self.send(prep, send_kwargs) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/sessions.py", line 645, in send r = adapter.send(request, kwargs) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/requests/adapters.py", line 517, in send raise SSLError(e, request=request) *requests.exceptions.SSLError: HTTPSConnectionPool(host='plantismash.secondarymetabolites.org', port=443): Max retries exceeded with url: /api/v1.0/version (Caused by SSLError(CertificateError("hostname 'plantismash.secondarymetabolites.org' doesn't match '.bioinformatics.nl'",),))**

What command did you issue? funannotate remote -m antismash -e *@gmail.com -g update_results/test.gbk -o functional_annotation --force -a plants**

Logfiles

08/23/22 10:41:38: OS: CentOS Linux 8, 256 cores, ~ 660 GB RAM. Python: 3.6.15 08/23/22 10:41:38: Running 1.8.13 08/23/22 10:41:38: Output directory functional_annotation already exists 08/23/22 10:41:38: Checking GenBank file for annotation

OS/Install Information

You are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.45 DBD::SQLite: 1.70 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.27 Getopt::Long: 2.52 Hash::Merge: 0.302 JSON: 4.02 LWP::UserAgent: 6.61 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.25 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 5.10 YAML: 1.30 local::lib: 2.000029 threads: 2.21 threads::shared: 1.59 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/zhangwenda/database/funannotate_db $PASAHOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/zhangwenda/biosoft/gene_prediction/gmes_linux_64_4 All 6 environmental variables are set

Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v36 diamond: 2.0.14 emapper.py: v1.0 ete3: 3.1.1 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.69_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.1-internal kallisto: 0.46.1 mafft: v7.490 (2021/Oct/30) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.0.33 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 26 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 37 external dependencies are installed

IanDMedeiros commented 2 years ago

Came across the same error today while trying to set up funannotate to work with both lichen mycobiont and photobiont genomes.

The problem seems to be that the plantismash API—if there even is one—is not set up like fungismash, i.e., http://plantismash.secondarymetabolites.org/api/v1.0/version, http://plantismash.secondarymetabolites.org/api/v1.0/stats, and http://plantismash.secondarymetabolites.org/api/v1.0/submit are not valid URLs.

Might be best to remove the plantismash option for now if there is not a functional API? I would think it should be fine to just submit through the web server and add the results in manually, although I haven't tested that yet.