MIBIG 4.0 compatibility problem #229
Comments
|
Hi Ruben, thanks for submitting this issue! BiG-SCAPE uses an antiSMASH processed version of the MIBiG genbank files. The pre-processed version of MIBiG 4.0 made available by the antiSMASH/MIBiG team is not available yet, hence why the download does not work for 4.0 instead of 3.1. To use that version, for now, you must process it with antiSMASH first (I expect second error is happening by giving BiG-SCAPE non antismash processed MIBiG files). I’d also recommend reading the MIBiG & References section of the wiki for more detail! |
|
This issue has not seen activity for 14 days and has been marked as stale. Please comment with additional information if this issue is still relevant. |
|
This issue has been stale for 14 days and has been closed. Please feel free to re-open this issue if necessary. |
After having the same error as #227 with
2.0.0-beta.1and cannot download the v4.0 of MIBIG, if done manually (downloading directly and changing the folder name to match the 3.1 automatic download) another error occurs. It seems its only compatibility problems, the antismash header version value in MIBIG 4.0 is changed to falseerror 1:
2024-12-15 20:24:06,599 INFO Downloading MIBiG version 4.0 Traceback (most recent call last): File "/home/ruben/BiG-SCAPE/bigscape.py", line 37, in <module> __main__.main() File "/home/ruben/BiG-SCAPE/big_scape/__main__.py", line 51, in main cli() File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/BiG-SCAPE/big_scape/cli/cluster_cli.py", line 159, in cluster run_bigscape(ctx.obj) File "/home/ruben/BiG-SCAPE/big_scape/run_bigscape.py", line 116, in run_bigscape mibig_version_dir = bs_files.get_mibig(run["mibig_version"], bigscape_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ruben/BiG-SCAPE/big_scape/file_input/load_files.py", line 61, in get_mibig download_dataset(mibig_url, mibig_dir, mibig_dir_compressed) File "/home/ruben/BiG-SCAPE/big_scape/file_input/load_files.py", line 87, in download_dataset raise ValueError("Could not download MIBiG file") ValueError: Could not download MIBiG fileerror 2
2024-12-15 20:22:25,008 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001987.gbk: Invalid antiSMASH version in GBK header Exception in thread Thread-6 (_handle_results): Traceback (most recent call last): File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/threading.py", line 1045, in _bootstrap_inner 2024-12-15 20:22:25,009 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0003006.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,009 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0002348.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,009 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000803.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,009 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001286.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,010 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001278.gbk: Invalid antiSMASH version in GBK header self.run() File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/threading.py", line 982, in run self._target(*self._args, **self._kwargs) File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/multiprocessing/pool.py", line 579, in _handle_results 2024-12-15 20:22:25,011 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001521.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,011 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001240.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,012 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000327.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,013 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001260.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,014 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000810.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,014 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000134.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,014 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0003077.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,014 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001724.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,014 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0002545.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,015 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000432.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,015 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0002360.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,016 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001093.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,016 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001634.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,016 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000905.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,016 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001026.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,017 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000257.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,017 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0001451.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,017 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0000528.gbk: Invalid antiSMASH version in GBK header 2024-12-15 20:22:25,018 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0002499.gbk: Invalid antiSMASH version in GBK header task = get() ^^^^^ File "/home/ruben/micromamba/envs/bigscape/lib/python3.11/multiprocessing/connection.py", line 251, in recv return _ForkingPickler.loads(buf.getbuffer()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: InvalidGBKError.__init__() takes 1 positional argument but 2 were given 2024-12-15 20:22:25,018 ERROR /home/ruben/BiG-SCAPE/big_scape/MIBiG/mibig_antismash_4.0_gbk/BGC0002692.gbk: Invalid antiSMASH version in GBK headerThe text was updated successfully, but these errors were encountered: