search

dongzhang0725 / PhyloSuite

PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
GNU General Public License v3.0
140 stars 24 forks source link

PhyloSuite not working #86

Open Gwendoline998 opened 7 months ago

Gwendoline998 commented 7 months ago

Hi, I am a new user of PhyloSuite, I tried to download nucleotide sequences from NCBI, but it does not work. The pop-up window is: The search failed for some of the sequences. As this may have been caused by a network problem, you can wait for a while and try again. If the problem persists you may report it at https://github.com/dongzhang0725/PhyloSuite/issues or send an email with the detailed traceback to dongzhang0725@gmail.com

thank you

Gwendoline998 commented 7 months ago

Traceback (most recent call last): File "src\Lg_SerhNCBI.py", line 493, in search File "Bio\Entrez__init.py", line 234, in esearch File "Bio\Entrez\init__.py", line 569, in _open File "urllib\request.py", line 223, in urlopen File "urllib\request.py", line 532, in open File "urllib\request.py", line 642, in http_response File "urllib\request.py", line 570, in error File "urllib\request.py", line 504, in _call_chain File "urllib\request.py", line 650, in http_error_default urllib.error.HTTPError: HTTP Error 500: Internal Server Error

dongzhang0725 commented 7 months ago

Hi, the best way to resolve this is to copy the sequence IDs in NCBI's search box in nucleotide database, then download the sequences and import them to PhyloSuite. see http://phylosuite.jushengwu.com/dongzhang0725.github.io/PhyloSuite-demo/five_ways_to_import/

Gwendoline998 @.***> 于2023年11月21日周二 18:12写道：

Traceback (most recent call last): File "src\LgSerhNCBI.py", line 493, in search File "Bio\Entrezinit.py", line 234, in esearch File "Bio\Entrezinit_.py", line 569, in _open File "urllib\request.py", line 223, in urlopen File "urllib\request.py", line 532, in open File "urllib\request.py", line 642, in http_response File "urllib\request.py", line 570, in error File "urllib\request.py", line 504, in _call_chain File "urllib\request.py", line 650, in http_error_default urllib.error.HTTPError: HTTP Error 500: Internal Server Error

— Reply to this email directly, view it on GitHub https://github.com/dongzhang0725/PhyloSuite/issues/86#issuecomment-1820611081, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADZXXOJZYKOOH4ATQDVV4A3YFR5A3AVCNFSM6AAAAAA7UI4NZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRQGYYTCMBYGE . You are receiving this because you are subscribed to this thread.Message ID: @.***>