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wonaya / ParaAT

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File names are too long #2

Open J-Calvelo opened 1 year ago

J-Calvelo commented 1 year ago

Hello, I found a problem. Because of how the file names work, it is possible to break the program with sufficiently large orthogroups

sh: 1: cannot create BG_IM_KAI8734412.1-BG_IM_KAI8742320.1-BG_IM_KAI8745906.1-BG_IM_KAI8745907.1-BG_IM_KAI8745909.1-BG_IM_KAI8745910.1-BG_IM_KAI8745911.1-BG_IM_KAI8745941.1-BG_IM_KAI8745942.1-BG_IM_KAI8745943.1-BG_IM_KAI8745944.1-BG_IM_KAI8745956.1-BGLB005059-PB-BGLB021092-PA-BGLB022082-PA-BGLB023327-PA-BGLB025331-PA-BGLB027520-PA-BGLB031420-PA-BGLB035763-PA-BGLB038275-PA-BGLB039474-PA-BG_iBS90_KAI8752803.1-BG_iBS90_KAI8779881.1-BG_iBS90_KAI8779882.1-BG_iBS90_KAI8779917.1-BG_iBS90_KAI8779919.1-BG_iBS90_KAI8779920.1-BG_iBS90_KAI8779921.1-BG_iBS90_KAI8779922.1-BG_iBS90_KAI8779925.1-BG_iBS90_KAI8779937.1-BP13038-RA.p1-BP22270-RA.p1-BP22271-RA.p1-BP22272-RA.p1-BP22288-RA.p1-BP22290-RA.p1-BP22294-RA.p1-BP22295-RA.p1-BP22296-RA.p1-Bstr_024387-T1-Bstr_024388-T1-Bstr_024389-T1-Bstr_024390-T1-Bstr_024406-T1-Bstr_024407-T1-Bstr_024882-T1-Bstr_049317-T1-BSUD.4130.3.p1-BSUD.4131.1.p1-BSUD.4136.1.p1-KAH9509203.1-KAH9509274.1-KAH9512184.1.pep_aln: File name too long

Wangchangsh commented 1 year ago

I got the same issue. Did you find a solution or alternative plan？

Wangchangsh commented 1 year ago

I've modified the naming to fit the Linux naming restrictions.

J-Calvelo commented 1 year ago

Hello. The Hyphy package has an utility script that does the same task https://github.com/veg/hyphy-analyses/tree/master/codon-msa

Wangchangsh commented 1 year ago

Thank you! Have a nice day!

On Tue, Apr 18, 2023 at 1:04 AM J-Calvelo @.***> wrote:

Hello. The Hyphy package has an utility script that does the same task https://github.com/veg/hyphy-analyses/blob/master/codon-msa/pre-msa.bf

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