Error: markers.bin not found in the folder

[Louis-MG]

Environment

• Installed via pip (include the output of pip list)
• Using a conda environment (include the output of conda list && conda list --revisions)
• Using a Docker container (include the IMAGE ID of the container)

conda_list_revisions.log

The error message:

[2026-02-06 13:40:25] INFO: GTDB-Tk v2.6.1                                                                                                                                                                                                                                                                                                            
[2026-02-06 13:40:25] INFO: gtdbtk classify_wf --genome_dir phylogeny_input_acnes --out_dir phylogeny_gtdbtk_output_acnes                                                                                                                                                                                                                             
[2026-02-06 13:40:25] INFO: Using GTDB-Tk reference data version r226: /mnt/scratch/LM/test_GTDBTK2/release226                                                                                                                                                                                                                                        
[2026-02-06 13:40:27] INFO: Loading reference genomes.                                                                                                                                                                                                                                                                                                
[2026-02-06 13:40:29] INFO: Calculating all vs all ANI with skani v0.3.1.                                                                                                                                                                                                                                                                             
[2026-02-06 13:40:29] INFO: Sketching refence genomes                                                                                                                                                                                                                                                                                                 
[2026-02-06 15:04:47] INFO: Done                                                                                                                                                                                                                                                                                                                      
[2026-02-06 15:04:47] ERROR: STDOUT:                                                                                                                                                                                                                                                                                                                  
[00:00:00.000] (7efed524f800) INFO   skani search -t 1 -d /tmp/gtdbtk78tz9ixl/sketch_ref --ql /tmp/gtdbtk78tz9ixl/query_list.txt --short-header -o /dev/stdout                                                                                                                                                                                        
[00:00:00.000] (7efed524f800) INFO   Searching...                                                                                                                                                                                                                                                                                                     
[00:00:00.000] (7efed524f800) ERROR  markers.bin not found in the folder. Ensure that the folder was generated by `skani sketch`.                                                                                                                                                                                                                     
[2026-02-06 15:04:53] ERROR: skani returned a non-zero exit code.                                                                                                                                                                                                                                                                                     
[2026-02-06 15:04:53] ERROR: Controlled exit resulting from an unrecoverable error or warning.                     

gtdbtk.log

I tried reinstalling skani just to check, I ran the test and check install commands and they ran fine. I re-downloaded the reference data as well to no avail.

[Louis-MG]

Update: installing via pip does not solve the problem. Downgrading to 2.6.0 did not work (pip)

[Louis-MG]

After digging a few seconds into the code, I found the solution : I had to change the tmpdir parameter.

[luoyixiao526]

After digging a few seconds into the code, I found the solution : I had to change the parameter.tmpdir

I met the same error, can you tell me how to deal with, thank you very much.

[Louis-MG]

After digging a few seconds into the code, I found the solution : I had to change the parameter.tmpdir

I met the same error, can you tell me how to deal with, thank you very much.

It is in the quote.

[luoyixiao526]

在代码里翻了几秒后，我找到了解决办法：我必须更改参数。tmpdir

我也遇到了同样的错误，你能告诉我该怎么处理吗？非常感谢。

yes, I see. I forgot to tell I get it, thank you.

[pchaumeil]

Hello,
In the next version of GTDB-Tk, the sketching step will actually be removed, as we plan to provide pre-sketched genomes as part of the database instead.
This will hopefully solve this problem.