During step13 there is an error. please help me

[suppakoko]

I executed below command. During step 13 "Createing InterPro tables" there is a error like below

yjko84@banana:~/analysis_tools/MicrobeAnnotator/bin$ microbeannotator_db_builder -d MicrobeAnnotator_DB -m blast -t 250 --step 13 --bin_path /home/yjko84/analysis_tools/MicrobeAnnotator/bin 2022-08-25 20:25:12,829 [INFO]: This is MicrobeAnnotator v2.0.5 2022-08-25 20:25:12,829 [INFO]: I will download and format the databases I use. 2022-08-25 20:25:12,829 [INFO]: Creating database folders 2022-08-25 20:25:12,829 [INFO]: Step 13 2022-08-25 20:25:12,829 [INFO]: Creating RefSeq to UniProt table 2022-08-25 20:27:31,768 [INFO]: Finished 2022-08-25 20:27:31,781 [INFO]: Creating KO to EC table 100% [..............................................................................] 50126 / 501262022-08-25 20:27:33,031 [INFO]: Finished 2022-08-25 20:27:33,031 [INFO]: Creating InterPro tables Traceback (most recent call last): File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 2450, in retrfile self.ftp.cwd(file) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/ftplib.py", line 638, in cwd return self.voidcmd(cmd) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/ftplib.py", line 280, in voidcmd return self.voidresp() File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/ftplib.py", line 253, in voidresp resp = self.getresp() File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/ftplib.py", line 248, in getresp raise error_perm(resp) ftplib.error_perm: 550 Failed to change directory.

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

Traceback (most recent call last): File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 1573, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 2452, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: <urlopen error ftp error: error_perm('550 Failed to change directory.')>

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/yjko84/anaconda3/envs/manno/bin/microbeannotator_db_builder", line 445, in main() File "/home/yjko84/anaconda3/envs/manno/bin/microbeannotator_db_builder", line 437, in main single_step, aspera, keep_temp, bin_path) File "/home/yjko84/anaconda3/envs/manno/bin/microbeannotator_db_builder", line 285, in database_duilder database_directory, interconversion_database) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/site-packages/microbeannotator/database/conversion_database_creator.py", line 156, in create_interpro_tables out=download_output) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/site-packages/wget.py", line 526, in download (tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 543, in _open '_open', req) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 1584, in ftp_open raise exc.with_traceback(sys.exc_info()[2]) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 1573, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/home/yjko84/anaconda3/envs/manno/lib/python3.7/urllib/request.py", line 2452, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: <urlopen error ftp error: URLError("ftp error: error_perm('550 Failed to change directory.')")>

Could you help me ?

[natashagriffin]

I just got this exact same error and have yet to figure it out. If I do I will update here! Hopefully someone else has already solved it.

[suppakoko]

I solved it. it was so simple. Just changed the link ftp://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz in the file $HOME/anaconda3/envs/manno/lib/python3.7/site-packages/microbeannotator/database/conversion_database_creator.py line number 155 Thanks

[natashagriffin]

Awesome!! Thank you so much for the fix, I had gone completely down the wrong troubleshooting path.

Did you succeed at running the step afterward? I tried to start step 13 over again but it seems to be stuck at the RefSeq to UniProt table creation step now. :/

Edit to update: Never mind! The first part of step 13 took ages for whatever reason, but it's now proceeding along with step 14. :)

[suppakoko]

Good luck! @natashagriffin

[gyeongjunCho]

I also had the same problem, but after applying @suppakoko's troubleshooting method, it was completely fixed.

thank you.