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+1! |
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hello, Did you solve the problem? how did you do to solve it? |
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There are some answers here. |
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Hello,
![image](https://private-user-images.githubusercontent.com/135034863/312074046-84fa7574-d448-4a13-888d-4fdf9216658b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjAzMjI4MzQsIm5iZiI6MTcyMDMyMjUzNCwicGF0aCI6Ii8xMzUwMzQ4NjMvMzEyMDc0MDQ2LTg0ZmE3NTc0LWQ0NDgtNGExMy04ODhkLTRmZGY5MjE2NjU4Yi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzA3JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcwN1QwMzIyMTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1hY2ZmYjZjYjEzNWI1NGRlYzRiYjYzZWZiNTUzMTNmMjM3YTc5OTlkODhkYWZkNTlhOTJlNzkyZTI4MTQ1MDExJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.pfHS0bQALXOb1AAEbzIyBKAEqqIyDD4XFA6D6jLN2u0)
When running according to the command “./bin/cafe5 --infile Orthogroups.GeneCount.cafe.tsv.new --tree cafe_formated.nwk --output_prefix cafe_result3 --cores 12 -k 3 -p --pvalue 0.05 &>k3.log‘’, an error will be reported,as shown in the following figure
After multiple cycles of deleting families, rerunning cafe5 still reports errors.
Then I tried to lower the lambda value ( 0.0001 ) (./bin/cafe5 --infile Orthogroups.GeneCount.cafe.tsv.new --tree cafe_formated.nwk --output_prefix cafe_result3 --cores 12 -k 3 -p -l 0.0001). Although it can run successfully, the result file is only three, excluding Gamma _ count.txt, etc.
![image](https://private-user-images.githubusercontent.com/135034863/312075949-8266aeb0-98c5-4e41-936e-636619d57af8.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjAzMjI4MzQsIm5iZiI6MTcyMDMyMjUzNCwicGF0aCI6Ii8xMzUwMzQ4NjMvMzEyMDc1OTQ5LTgyNjZhZWIwLTk4YzUtNGU0MS05MzZlLTYzNjYxOWQ1N2FmOC5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzA3JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcwN1QwMzIyMTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT0wMWYzNjlmNjc5NDZkY2Q1M2EzNTU2YjYwMjM3OThkOTFiMjMzOWM3Yjc1NjJiNDY0NjBkZmNmZTM2MGQ0ZTJmJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.ObROqLdLD9QAHEUiX0vuzml1sMU4PuBYtikPV5SnV9k)
Can you give me some adivce?
Thanks.
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