PhyloSuite
PhyloSuite copied to clipboard
dongzhang0725
unforeseen problem-extraction GB files
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
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.
— Reply to this email directly, view it on GitHub https://github.com/dongzhang0725/PhyloSuite/issues/89#issuecomment-1905777280, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIZ6BNVBKBDQ3JRNTKS4EO3YP6INVAVCNFSM6AAAAABCGVODUWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBVG43TOMRYGA . You are receiving this because you authored the thread.Message ID: @.***>
-- Kindest regards,
Mgr. Chahrazed Rahmouni, PhD. Masaryk University Faculty of Science Department of Botany and Zoology Parasitology Group University Campus Bohunice Kamenice 753/5 Building A31, N° 333 625 00 Brno Czech Republic
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