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gamcil / cblaster

Find clustered hits from a BLAST search
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Repeated failure of search at results retrieving stage: #108

Open jarnie58 opened 2 months ago

jarnie58 commented 2 months ago

Repeated failure of search at results retrieving stage: S C:\Users\jarni\OneDrive - O365 Turun yliopisto\Documents\Dec18> cblaster search -qf .\modifiers_pseudocluster_dec18.fasta -p plot.html -s session.json Importing genomicsqlite failed, falling back to SQLite3 [09:17:46] INFO - Starting cblaster in remote mode [09:17:46] INFO - Launching new search [09:17:47] INFO - Request Identifier (RID): 89V8A7H5013 [09:17:47] INFO - Request Time Of Execution (RTOE): 22s [09:18:09] INFO - Polling NCBI for completion status [09:18:09] INFO - Checking search status... [09:19:09] INFO - Checking search status... [09:20:09] INFO - Checking search status... [09:21:09] INFO - Checking search status... [09:22:09] INFO - Checking search status... [09:23:09] INFO - Checking search status... [09:24:09] INFO - Checking search status... [09:25:09] INFO - Checking search status... [09:26:09] INFO - Checking search status... [09:26:11] INFO - Search has completed successfully! [09:26:11] INFO - Retrieving results for search 89V8A7H5013 Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "C:\Users\jarni\AppData\Local\Programs\Python\Python312\Scripts\cblaster.exe__main__.py", line 7, in File "C:\Users\jarni\AppData\Local\Programs\Python\Python312\Lib\site-packages\cblaster\main.py", line 432, in main cblaster( File "C:\Users\jarni\AppData\Local\Programs\Python\Python312\Lib\site-packages\cblaster\main.py", line 318, in cblaster rid, results = remote.search( ^^^^^^^^^^^^^^ File "C:\Users\jarni\AppData\Local\Programs\Python\Python312\Lib\site-packages\cblaster\remote.py", line 371, in search results = retrieve(rid, hitlist_size=hitlist_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jarni\AppData\Local\Programs\Python\Python312\Lib\site-packages\cblaster\remote.py", line 209, in retrieve .group(1) ^^^^^ AttributeError: 'NoneType' object has no attribute 'group' PS C:\Users\jarni\OneDrive - O365 Turun yliopisto\Documents\Dec18>

Rene-Hoover commented 1 month ago

I'm not sure if this can help you or other folks investigating the issue, but I received the same error for 1 of 2 query files I was analyzing. This let me trouble shoot my files and when I compared my input it seemed like having a blank line in between the sequences was the problem.

For example, the file with spaces between:

>fasta-header-1
MSINYKEVINDLRTQLGDRPVTD

>fasta-header-2
RAAGTSLSGQAIGEGILLILGHDGFRKIEVSS

>fasta-header-3
ALAERIRKKYSIKNTTGYGINS

Did not work, but if I removed the spaces between lines like so:

>fasta-header-1
MSINYKEVINDLRTQLGDRPVTD
>fasta-header-2
RAAGTSLSGQAIGEGILLILGHDGFRKIEVSS
>fasta-header-3
ALAERIRKKYSIKNTTGYGINS

It ran without error.

I'm just a user, but this is what worked for me. Cheers!