celine-mercier
commented
1 year ago Hello, The right place for OBITools3 issues is here: https://git.metabarcoding.org/obitools/obitools3/-/issues/ It looks like that file is corrupted, can you try downloading it again? Cheers Celine
Hi! Celine Mercier Recently, STD_INV_13.dat.gz was downloaded from the EMBL database. When I try to import STD_INV_13.dat.gz from the Wolf tutorial to Build a reference database, either on Mac Terminal or Linux system, I get the following error:
(obi3-env)@ [aspinus]$ obi import --embl EMBL coi_embl2023/embl_refs 2023-03-21 09:22:05,456 [import : INFO ] obi import: imports an object (file(s), obiview, taxonomy...) into a DMS 2023-03-21 09:22:05,471 [import : INFO ] Importing an unknown number of entries Parsing file EMBL/STD_INV_11.dat.gz (1/13) 2023-03-21 09:22:07,994 [import : INFO ] Imported 0 entries 2023-03-21 09:22:16,768 [import : INFO ] Imported 50000 entries ………… ………… …………
Parsing file EMBL/STD_INV_13.dat.gz (13/13) 2023-03-21 13:06:30,239 [import : INFO ] Imported 12250000 entries 2023-03-21 13:06:52,489 [import : INFO ] Imported 12300000 entries Traceback (most recent call last): File "/data/home/obitools3/obi3-env/bin/obi", line 4, in
import('pkg_resources').run_script('OBITools3==3.0.1b21', 'obi')
File "/data/home/obitools3/obi3-env/lib/python3.8/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/data/home/obitools3/obi3-env/lib/python3.8/site-packages/pkg_resources/init.py", line 1462, in run_script
exec(code, namespace, namespace)
File "/data/home/obitools3/obi3-env/lib/python3.8/site-packages/OBITools3-3.0.1b21-py3.8-linux-x86_64.egg/EGG-INFO/scripts/obi", line 62, in
config[root_config_name]['module'].run(config)
File "python/obitools3/commands/import.pyx", line 333, in obitools3.commands.import.run
File "python/obitools3/parsers/embl.pyx", line 186, in emblIterator_dir
File "python/obitools3/parsers/embl.pyx", line 143, in emblIterator_file
File "python/obitools3/files/linebuffer.pyx", line 22, in iter
File "/usr/local/lib/python3.8/gzip.py", line 384, in readline
return self._buffer.readline(size)
File "/usr/local/lib/python3.8/_compression.py", line 68, in readinto
data = self.read(len(byte_view))
File "/usr/local/lib/python3.8/gzip.py", line 481, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid distance code
Any advice given would be greatly appreciated and thanks for your work on OBITools! Aspinus