运行trf 总是在运行一段时间后退出且查看nohup.out发现没有报错。

[Blosers]

我输入的命令是trf s.fasta 2 5 7 80 10 50 2000 -l 15

以下是nohup.out的内容
Copyright (C) Dr. Gary Benson 1999-2012. All rights reserved.

Loading sequence...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 1...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 2...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 3...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 4...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 5...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 6...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 7...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 8...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 9...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 10...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 11...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 12...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 13...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 14...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 15...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Initializing data structures...
Computing TR Model Statistics...
Scanning Sequence 16...
Freeing Memory...
Resolving output...
Done.
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很抱歉，实在是不明白为什么会突然出现这样的结果（存在太多省略号），其次输出的结果文件太多，超过26000个文件且都是.html 或 txt.html

[gitforp]

您好，我使用trf时遇到了和您一样的问题，请问您的问题解决了吗？方便请教一下您是怎么解决的吗？

[Blosers]

抱歉，那个这个问题我也没有解决，后续就放弃了，实在是抱歉啊。   印痕 ***@***.***  

…

------------------ 原始邮件 ------------------ 发件人: ***@***.***>; 发送时间: 2024年6月5日(星期三) 上午8:39 收件人: ***@***.***>; 抄送: ***@***.***>; ***@***.***>; 主题: Re: [Benson-Genomics-Lab/TRF] 运行trf 总是在运行一段时间后退出且查看nohup.out发现没有报错。 (Issue #22) 您好，我使用trf时遇到了和您一样的问题，请问您的问题解决了吗？方便请教一下您是怎么解决的吗？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[gitforp]

感谢您的回复，我检查结果时发现结果中是包含基因组序列的.masked文件的，而且我的基因组文件是16条序列，输出日志也显示是处理了16条序列，所以我有个猜测：是不是软件已经完成了检测并进行了mask？请问您的基因组序列是16条吗

[Blosers]

是的，我的染色体数目也是16条   印痕 ***@***.***  

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------------------ 原始邮件 ------------------ 发件人: ***@***.***>; 发送时间: 2024年6月6日(星期四) 下午4:52 收件人: ***@***.***>; 抄送: ***@***.***>; ***@***.***>; 主题: Re: [Benson-Genomics-Lab/TRF] 运行trf 总是在运行一段时间后退出且查看nohup.out发现没有报错。 (Issue #22) 感谢您的回复，我检查结果时发现结果中是包含基因组序列的.masked文件的，而且我的基因组文件是16条序列，输出日志也显示是处理了16条序列，所以我有个猜测：是不是软件已经完成了检测并进行了mask？请问您的基因组序列是16条吗 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[miaoxm2]

我之前也遇到了同样的问题，最近发现改用最新版本4.10.0后就能成功跑完程序。详见更新日志：TRF now has an exit status of 0 on success, and non-zero otherwise. Previously, TRF would have a non-zero exit status which was to be interpreted by the user as the number of TRs processed. However, this is impractical since the maximum value an exit status might take is 255.