TRF不报错就停止运行的问题 #24
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怎么停止？没有进程运行？ |
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我是通过qsub提交的，qstat显示已经没有运行了
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王梓颖
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| 发送日期 | 2025年3月4日 16:31 |
| 收件人 | ***@***.***> |
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| 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |
怎么停止？没有进程运行？ps xuf能看到正在运行的子命令吗？
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zhangrengang left a comment (zhangrengang/Centromics#24)
怎么停止？没有进程运行？ps xuf能看到正在运行的子命令吗？
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本地运行下看看呢？ |
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前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果
---- 回复的原邮件 ----
| 发件人 | ***@***.***> |
| 发送日期 | 2025年03月04日 20:48 |
| 收件人 | zhangrengang/Centromics ***@***.***> |
| 抄送人 | uumnoi ***@***.***>,
Author ***@***.***> |
| 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |
本地运行下看看呢？
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zhangrengang left a comment (zhangrengang/Centromics#24)
本地运行下看看呢？
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我依旧没明白你遇到了啥问题。log到这就退出了吗？也不报错？
…----- Original Message -----
From: uumnoi ***@***.***>
To: zhangrengang/Centromics ***@***.***>
Cc: zhangrengang ***@***.***>, Comment ***@***.***>
Sent: Tue, 04 Mar 2025 04:55:07 -0800
Subject: Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24)
前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***>
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uumnoi left a comment (zhangrengang/Centromics#24)
前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***>
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是的，多次都是从这里就退出了，log里没有提示任何报错
…---- 回复的原邮件 ----
| 发件人 | ***@***.***> |
| 发送日期 | 2025年03月05日 06:23 |
| 收件人 | zhangrengang/Centromics ***@***.***> |
| 抄送人 | uumnoi ***@***.***>,
Author ***@***.***> |
| 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |
我依旧没明白你遇到了啥问题。log到这就退出了吗？也不报错？<br> <br> <br> <br> ----- Original Message -----<br> From: uumnoi ***@***.***><br> To: zhangrengang/Centromics ***@***.***><br> Cc: zhangrengang ***@***.***>, Comment ***@***.***><br> Sent: Tue, 04 Mar 2025 04:55:07 -0800<br> Subject: Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24)<br> <br> 前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you commented.Message ID: ***@***.***><br> <br> uumnoi left a comment (zhangrengang/Centromics#24)<br> 前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you commented.Message ID: ***@***.***>
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zhangrengang left a comment (zhangrengang/Centromics#24)
我依旧没明白你遇到了啥问题。log到这就退出了吗？也不报错？<br> <br> <br> <br> ----- Original Message -----<br> From: uumnoi ***@***.***><br> To: zhangrengang/Centromics ***@***.***><br> Cc: zhangrengang ***@***.***>, Comment ***@***.***><br> Sent: Tue, 04 Mar 2025 04:55:07 -0800<br> Subject: Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24)<br> <br> 前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you commented.Message ID: ***@***.***><br> <br> uumnoi left a comment (zhangrengang/Centromics#24)<br> 前几次运行的时候没有DRMAA包，日子显示为本地运行，后几次安装了此包，但都是同样的结果<br> ---- 回复的原邮件 ----<br> | 发件人 | ***@***.***> |<br> | 发送日期 | 2025年03月04日 20:48 |<br> | 收件人 | zhangrengang/Centromics ***@***.***> |<br> | 抄送人 | uumnoi ***@***.***>,<br> Author ***@***.***> |<br> | 主题 | Re: [zhangrengang/Centromics] TRF不报错就停止运行的问题 (Issue #24) |<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> zhangrengang left a comment (zhangrengang/Centromics#24)<br> <br> 本地运行下看看呢？<br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you authored the thread.Message ID: ***@***.***><br> <br> —<br> Reply to this email directly, view it on GitHub, or unsubscribe.<br> You are receiving this because you commented.Message ID: ***@***.***>
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看看'/data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/cmds.list.out'里的log |
data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf文件夹没有out，只有多个fasta，一个cmds.list，一个空的cmds.list.completed |
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很奇怪。是最新版本吗？ |
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版本是0.4 |
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试试github的最新版？我目前也不知问题出在哪 |
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张老师您好！
我在使用您的软件时遇到了运行到如下情况就不报错停止的问题，
25-03-04 15:07:17 [INFO] Run TRF to identify tandem repeats in reads
25-03-04 15:25:17 [INFO] 64 commands in /data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/cmds.list, 0 commands in /data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/cmds.list.completed
25-03-04 15:25:17 [INFO] continue to run 64 commands
25-03-04 15:25:17 [INFO] VARS: {'tc_tasks': 32, 'mode': 'local', 'grid_opts': '-tc {tc}', 'cpu': 1, 'mem': '1g', 'cont': True, 'retry': 1, 'script': None, 'out_path': '/data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/cmds.list.out', 'completed': '/data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/cmds.list.completed', 'cmd_sep': '\n\n\n', 'kargs': {}}
25-03-04 15:25:17 [INFO] running 64 commands: try 1
25-03-04 15:25:17 [INFO] reset tc_tasks to 32 by [32, 96, 4164, 64]
确认了环境没问题，随即在cmds.list里找一条命令如cd /data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf && trf /data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/chunks.11.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /data2/jiyu/xiaomaiassembly/23ZF31219/centromics/tmp/centomics.trf/chunks.11.fasta.*.dat
也可以正常运行
多次尝试都是同样情况，请问原因是什么？
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