Error during "Fetching genomic context"

[Adwaith99]

In the version, 1.3.15, I am getting the error as shown below.

Importing genomicsqlite failed, falling back to SQLite3 [10:55:14] INFO - Starting cblaster in remote mode [10:55:14] INFO - Launching new search [10:55:15] INFO - Request Identifier (RID): NFY6JRSY013 [10:55:15] INFO - Request Time Of Execution (RTOE): 30s [10:55:45] INFO - Polling NCBI for completion status [10:55:45] INFO - Checking search status... [10:56:45] INFO - Checking search status... [10:57:45] INFO - Checking search status... [10:58:45] INFO - Checking search status... [10:59:45] INFO - Checking search status... [11:00:45] INFO - Checking search status... [11:01:45] INFO - Checking search status... [11:01:45] INFO - Search has completed successfully! [11:01:45] INFO - Retrieving results for search NFY6JRSY013 [11:06:32] INFO - Parsing results... [11:06:32] INFO - Found 13382 hits meeting score thresholds for remote search [11:06:32] INFO - Fetching genomic context of hits Traceback (most recent call last): File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.2288.0_x64__qbz5n2kfra8p0\lib\runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.2288.0_x64qbz5n2kfra8p0\lib\runpy.py", line 86, in _run_code exec(code, run_globals) File "C:\Users\adwai\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\Scripts\cblaster.exe\main__.py", line 7, in File "C:\Users\adwai\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\cblaster\main.py", line 432, in main cblaster( File "C:\Users\adwai\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\cblaster\main.py", line 334, in cblaster organisms = context.search( File "C:\Users\adwai\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\cblaster\context.py", line 591, in search rows = efetch_IPGs( File "C:\Users\adwai\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\cblaster\context.py", line 91, in efetch_IPGs if handle.code != 200: AttributeError: '_io.TextIOWrapper' object has no attribute 'code'. Did you mean: 'close'?

[gamcil]

I'm having the same issue, it looks like there is a problem on the NCBI's side (E-utilities request for identical proteins is returning GenBank records...). Might just have to wait a little bit for it to be resolved unfortunately

[Adwaith99]

Hi, Just wanted to confirm, the error still has not been resolved right?

Thank you

[gamcil]

Should be resolved as of the new release which is available now (https://github.com/gamcil/cblaster/releases/tag/v1.3.16). Could you try it out and see if it is working for you?

[Adwaith99]

Hi, It is working now. Thank you so much. @gamcil

[gamcil]

Happy to hear it, will close this issue.