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dongzhang0725 / PhyloSuite

PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
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unforeseen problem-extraction GB files #89

Open Gwendoline998 opened 5 months ago

Gwendoline998 commented 5 months ago

Hi, I am trying to extract GenBank files, but not working (see below)

No features could be found in these IDs: MW666182_G_mediotorus_new_variant_N_texanus_WI_USA, MT879676_Gyrodactylus_ticuchi_Notropis_moralesi_Mexico_Cypriniformes_Leuciscidae, MT879671_Gyrodactylus_tobala_Notropis_imeldae_Mexico_Cypriniformes_Leuciscidae, MH667466_Gyrodactylus_sp_Misgurnus_anguillicaudatus_USA_Cypriniformes_Cobitidae, MH667465_Gyrodactylus_sp_Misgurnus_anguillicaudatus_USA_Cypriniformes_Cobitidae, KT149288_Gyrodactylus_sp_Notemigonus_crysoleucas_Minnesota_Cypriniformes_Leuciscidae, KF263527_Gyrodactylus_laevisoides_Canada_Phoxinus_eos_Cypriniformes_Leuciscidae, KF178301_G_mediotorus_original_description_N_hudsonius_CANADA, HQ738514_Ieredactylus_rivuli_Rivulus_hartii_Cyprinodontiformes_Rivulidae_Trinidad, HF548678_Laminiscus_gussevi_Iceland, Gyrodactylus_wardi_CaCo15, Gyrodactylus_variabilis_NoCr18, Gyrodactylus_stunkardi_GNY15_GNY18, Gyrodactylus_spathulatus_GNY2, Gyrodactylus_sp_Hnuchalis_GMI1, Gyrodactylus_sp_Cneogaeus_GWI3, Gyrodactylus_sp2_Ratratulus_GNY14, Gyrodactylus_sp2_Cspadiceum_GAR10, Gyrodactylus_sp1_Ratratulus_GNY12_GNY13, Gyrodactylus_sp1_Cspadiceum_GAR8, Gyrodactylus_scholzi_GNY9n_GNY10, Gyrodactylus_prikrylovae_GNY8, Gyrodactylus_mendeli_GWI7_GWI8, Gyrodactylus_lummei_GAR6_GAR7_GAR9, Gyrodactylus_kuchtai_GWI1_GWI2, Gyrodactylus_huyseae_GAR2_GAR3_GAR4, Gyrodactylus_hanseni_GAR1, Gyrodactylus_hamdii_GNY16, Gyrodactylus_ellae_GNY3_GNY4_GNY17, Gyrodactylus_dechtiari_GNY6, Gyrodactylus_colemanensis_GNY1, Gyrodactylus_atratuli_RhCaAS2_15RhAt1_6_AS2, AY099508_Gyrodactylus_sp_Rhinichthys_osculus_Usa_Idaho_snake_river_Cypriniformes_Leuciscidae, 3_5_9_CYVE_143_CYVE_15_NOST_2_Gyrodactylus_ITS, 4_7_CYVE_10_Gyrodactylus_ITS, KT149287_G_crysoleucas_N_crysoleucas_MINNESOTA_USA

dongzhang0725 commented 5 months ago

The listed IDs don't have gene annotations.

Gwendoline998 commented 5 months ago

Hi,

even a search on NCBI failed, see below

Traceback (most recent call last):

File "urllib\request.py", line 1318, in do_open

File "http\client.py", line 1239, in request

File "http\client.py", line 1285, in _send_request

File "http\client.py", line 1234, in endheaders

File "http\client.py", line 1026, in _send_output

File "http\client.py", line 964, in send

File "http\client.py", line 1400, in connect

File "ssl.py", line 407, in wrap_socket

File "ssl.py", line 817, in init

File "ssl.py", line 1077, in do_handshake

File "ssl.py", line 689, in do_handshake

ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)

During handling of the above exception, another exception occurred:

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 526, in open

File "urllib\request.py", line 544, in _open

File "urllib\request.py", line 504, in _call_chain

File "urllib\request.py", line 1361, in https_open

File "urllib\request.py", line 1320, in do_open

urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)>

Le mar. 23 janv. 2024 à 11:47, zhang dong @.***> a écrit :

The listed IDs don't have gene annotations.

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dongzhang0725 commented 5 months ago

Hi @Gwendoline998 ,

It is caused by your network problem. You can try to download sequences from NCBI webpage, then import the downloaded files into PhyloSuite. Check http://phylosuite.jushengwu.com/dongzhang0725.github.io/PhyloSuite-demo/five_ways_to_import/ for details.

Hope it helps, Dong

dongzhang0725 commented 5 months ago

Also, check if this method help: image image