bgdata.errors.TagNotFound: Tag master for package genomicscores/caddpack/1.0 not found

[Conghui2023]

Hi, when I run the 'run.sh' on the 'example' you provided, I encountered this problem, do you know the reason, and how can I solve it?

Traceback (most recent call last):
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/bin/oncodrivefml", line 11, in
sys.exit(cmdline())
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/oncodrivefml/main.py", line 104, in cmdline
override_config)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/oncodrivefml/main.py", line 39, in main
configuration = load_configuration(config_file, override=config_override_dict)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/oncodrivefml/config.py", line 33, in load_configuration
return BGConfig(config_template, config_file=config_file, use_env_vars=True, override_values=override, unrepr=False)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgconfig.py", line 232, in init
res = self.validate(Validator(), preserve_errors=True)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/configobj/init.py", line 2301, in validate
check = self.validate(validator, preserve_errors=preserve_errors, copy=copy, section=section[entry])
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/configobj/init.py", line 2254, in validate
val = section[entry]
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/configobj/init.py", line 552, in getitem
return self._interpolate(key, val)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/configobj/init.py", line 544, in _interpolate
return engine.interpolate(key, value)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgconfig.py", line 60, in interpolate
value = self.bgdata_engine.interpolate(key, value)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgdata/configobj.py", line 46, in interpolate
path = bgdata.get(match.group(1))
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgdata/manager.py", line 220, in get
return self._get(project, dataset, version, ref)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgdata/manager.py", line 201, in _get
build = self._ref2build(pkg, ref)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgdata/manager.py", line 157, in _ref2build
build = self._tag2build(pkg, ref)
File "/share/home/luoylLab/liconghui/.conda/envs/oncodrivefml_env/lib/python3.7/site-packages/bgdata/manager.py", line 143, in _tag2build
raise TagNotFound(err_msg)
bgdata.errors.TagNotFound: Tag master for package genomicscores/caddpack/1.0 not found (HTTPSConnectionPool(host='bbglab.irbbarcelona.org', port=443): Max retries exceeded with url: /bgdata/genomicscores/caddpack/1.0.master?e427999cf3e8c5371a16ed911bdd02 (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x2b8f28256f10>: Failed to resolve 'bbglab.irbbarcelona.org' ([Errno -2] Name or service not known)")))

[FedericaBrando]

Hi, Thanks for reporting the error.

Could you try another time, sometimes the connection with the bbglab.irbbarcelona.org is lost and then recovered.

Please let me know if the error persists.

[Conghui2023]

Hi, I just tried it again, but the error persists. 2024年11月13日 00:08，Federica Brando ***@***.***> 写道： Du får ikke ofte mails fra ***@***.*** Få mere at vide om, hvorfor dette er vigtigt<https://aka.ms/LearnAboutSenderIdentification> Hi, Thanks for reporting the error. Could you try another time, sometimes the connection with the bbglab.irbbarcelona.org is lost and then recovered. Please let me know if the error persists. — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCBSD7JQVTT2LK2HB7JMZDD2AIRXBAVCNFSM6AAAAABRTBHMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZQHEZTSOJXG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[FedericaBrando]

I see, can you provide me the version of oncodrivefml you are trying to run? Thanks

[Conghui2023]

Many thanks for your continued support, the version is 2.1.3 发自我的 iPhone 在 2024年11月13日，19:52，Federica Brando ***@***.***> 写道：  Du får ikke ofte mails fra ***@***.*** Få mere at vide om, hvorfor dette er vigtigt<https://aka.ms/LearnAboutSenderIdentification> I see, can you provide me the version of oncodrivefml you are trying to run? Thanks — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCBSD7LWKGBLL6KZ6KZFAWD2AM4PXAVCNFSM6AAAAABRTBHMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTGM4TGMJQGE>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[FedericaBrando]

could you try again with the latest oncodrivefml version (2.4.0) downloaded from pip?

[Conghui2023]

I tried it again with 2.4.0 version as you suggested, but unfortunately, the issue still existed. 发自我的 iPhone 在 2024年11月13日，22:41，Federica Brando ***@***.***> 写道：  Du får ikke ofte mails fra ***@***.*** Få mere at vide om, hvorfor dette er vigtigt<https://aka.ms/LearnAboutSenderIdentification> could you try again with the latest oncodrivefml version (2.4.0) downloaded from pip? — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCBSD7IZU2GIMNIKKDTFIYD2ANQIVAVCNFSM6AAAAABRTBHMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTHAYTGMJSGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[FedericaBrando]

Can you confirm that you can access the following website:
bbglab.irbbarcelona.org

[Conghui2023]

Yes, I can access this website. 2024年11月14日 00:11，Federica Brando ***@***.***> 写道： Can you confirm that you can access the following website: bbglab.irbbarcelona.org<https://bbglab.irbbarcelona.org/> — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCBSD7ODJ7N3CCDQILUDYRD2AN22PAVCNFSM6AAAAABRTBHMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZUGA3DIOBQGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Conghui2023]

Hi, in this case, could you please directly provide us with the download links for reference and other required documents? Thank you very much in advance All the best, Conghui 发自我的 iPhone 在 2024年11月14日，09:29，Conghui Li ***@***.***> 写道：  Yes, I can access this website. 2024年11月14日 00:11，Federica Brando ***@***.***> 写道： Can you confirm that you can access the following website: bbglab.irbbarcelona.org<https://bbglab.irbbarcelona.org/> — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCBSD7ODJ7N3CCDQILUDYRD2AN22PAVCNFSM6AAAAABRTBHMM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZUGA3DIOBQGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[FedericaBrando]

Hi,

You can try the following approach:

Before running OncodriveFML, you can download the data first with these commands [source]:

1. Remove the ~/.bgdata folder
2. Downloading the cadd scores:

   bgdata get genomicscores/caddpack/1.0

3. Downloading the genome reference:

   bgdata get datasets/genomereference/hg19

4. export BGDATA_LOCAL=~/.bgdata and BGDATA_OFFLINE=TRUE environment variables
5. modify the ./run.sh file to run with the --debug flag (so we are able to see what is going on in the run)
6. run the example.

Please can you also ping bbglab.irbbarcelona.org to check that is indeed reachable from your terminal? Thanks

[Conghui2023]

Hi, The method you provided works, thanks a million! BTW, when I run ‘ping bbglab.irbbarcelona.org’ ,it is indeed reachable. I think it may be because my Linux environment network is not stable, so I can not download reference directly through run.sh.

…

2024年11月18日 18:36，Federica Brando ***@***.***> 写道： Hi, You can try the following approach: Before running OncodriveFML, you can download the data first with these commands [source]: • Remove the ~/.bgdata folder • Downloading the cadd scores: bgdata get genomicscores/caddpack/1.0 • Downloading the genome reference: bgdata get datasets/genomereference/hg19 • export BGDATA_LOCAL=~/.bgdata and BGDATA_OFFLINE=TRUE environment variables • modify the ./run.sh file to run with the --debug flag (so we are able to see what is going on in the run) • run the example. Please can you also ping bbglab.irbbarcelona.org to check that is indeed reachable from your terminal? Thanks — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>