rep21 ValueError: Please check subsample directory and try again

[Zoule7]

when I run $ skmer correct -main dimtrx_main.txt -sub subsample
rep21
ValueError: Please check subsample directory and try again

could you please tell what happened and how to solve it? I tried to repeat the run many times, the previous steps were no problem, always wrong here. thank you.

[octpalacios]

Hi,
I'm experiencing the same problem. Have you managed to find a solution?

[ClementJeanjean]

Hi, I faced the same issue, which is due to the deprecation of pd.df.append() function (line 659 in main.py) with the pandas version > 2. Then two options are possible,
(i) either (before installing skmer) an older version (v < 2) of pandas need to be installed in skmer environment (e.g. conda install pandas=1.5.2 ),
(ii) replace line 659 'combo_results_df = combo_results_df.append(result_dfm, ignore_index = True)' in /path/to/conda/envs/skmer/main.py by 'combo_results_df = pd.concat([combo_result_df, result_dfm], ignore_index = True)'

[leone93]

Yes, as @ClementJeanjean suggest the error is this one:

skmer --debug  correct -p 16 -main dimtrx_main.txt -sub subsample
rep18
Traceback (most recent call last):
File "/ibex/user/fabbial/conda-environments/kmer/lib/python3.12/site-packages/skmer/__main__.py", line 659, in correction
     combo_result_df = combo_result_df.append(result_dfm, ignore_index = True)
                       ^^^^^^^^^^^^^^^^^^^^^^
   File "/ibex/user/fabbial/conda-environments/kmer/lib/python3.12/site-packages/pandas/core/generic.py", line 6299, in __getattr__
     return object.__getattribute__(self, name)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

and be corrected changing :

 combo_result_df = combo_result_df.append(result_dfm, ignore_index = True)
` with: `
combo_result_df = pd.concat([combo_result_df, result_dfm], ignore_index = True)

in your/skmer/path/skmer/main.py

[Zoule7]

I have received your mail. Thank you very much for your help. 邹乐 ***@***.***

…

------------------ Original ------------------ From: ClementJeanjean ***@***.***&gt; Date: Wed,Apr 2,2025 8:50 PM To: shahab-sarmashghi/Skmer ***@***.***&gt; Cc: Zoule7 ***@***.***&gt;, Author ***@***.***&gt; Subject: Re: [shahab-sarmashghi/Skmer] rep21 ValueError: Please checksubsample directory and try again (Issue #30) Hi, I faced the same issue, which is due to the deprecation of pd.df.append() function (line 659 in main.py) with the pandas version &gt; 2. Then two options are possible, (i) either (before installing skmer) an older version (v < 2) of pandas need to be installed in skmer environment (e.g. conda install pandas=1.5.2 ), (ii) replace line 659 'combo_results_df = combo_results_df.append(result_dfm, ignore_index = True)' in /path/to/conda/envs/skmer/main.py by 'combo_results_df = pd.concat([combo_result_df, result_dfm], ignore_index = True)' — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt; ClementJeanjean left a comment (shahab-sarmashghi/Skmer#30) Hi, I faced the same issue, which is due to the deprecation of pd.df.append() function (line 659 in main.py) with the pandas version &gt; 2. Then two options are possible, (i) either (before installing skmer) an older version (v < 2) of pandas need to be installed in skmer environment (e.g. conda install pandas=1.5.2 ), (ii) replace line 659 'combo_results_df = combo_results_df.append(result_dfm, ignore_index = True)' in /path/to/conda/envs/skmer/main.py by 'combo_results_df = pd.concat([combo_result_df, result_dfm], ignore_index = True)' — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;

[Zoule7]

I have received your mail. Thank you very much.&nbsp; 邹乐 ***@***.***

…

------------------ Original ------------------ From: leone93 ***@***.***&gt; Date: Wed,May 14,2025 8:37 PM To: shahab-sarmashghi/Skmer ***@***.***&gt; Cc: Zoule7 ***@***.***&gt;, Author ***@***.***&gt; Subject: Re: [shahab-sarmashghi/Skmer] rep21 ValueError: Please checksubsample directory and try again (Issue #30) leone93 left a comment (shahab-sarmashghi/Skmer#30) Yes, as @ClementJeanjean suggest the error is this one: skmer --debug correct -p 16 -main dimtrx_main.txt -sub subsample rep18 Traceback (most recent call last): File "/ibex/user/fabbial/conda-environments/kmer/lib/python3.12/site-packages/skmer/main.py", line 659, in correction combo_result_df = combo_result_df.append(result_dfm, ignore_index = True) ^^^^^^^^^^^^^^^^^^^^^^ File "/ibex/user/fabbial/conda-environments/kmer/lib/python3.12/site-packages/pandas/core/generic.py", line 6299, in getattr return object.getattribute(self, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'? and be corrected changing combo_result_df = combo_result_df.append(result_dfm, ignore_index = True) with: combo_result_df = pd.concat([combo_result_df, result_dfm], ignore_index = True) in your/skmer/path/skmer/main.py — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;