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OpenGene / GeneFuse

Gene fusion detection and visualization
MIT License
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while running Stuck #30

Open hulai-hulai opened 3 years ago

hulai-hulai commented 3 years ago

hi, Sometimes it gets stuck and does not run. The final state is as follows. and the task is suspended. Why is it? Please help me, thanks! 23:11:23 start with 4 threads 23:11:27 mapper indexing done

grafitos commented 3 years ago

Hi,

Same behavior,

sudo strace -p 1136 strace: Process 1136 attached futex(0x7ffdbdfee018, FUTEX_WAIT_PRIVATE, 0, NULL

sudo strace -p 1134 strace: Process 1134 attached futex(0x7ffdbdfee018, FUTEX_WAIT_PRIVATE, 0, NULL

Fabrice

amacbride commented 2 years ago

It's most likely a threading issue -- I found that 32-36 threads hangs, but when I tried 1, 2, 4, 8, 16, and 24 it worked fine.

asmlgkj commented 2 years ago

16 does not work for me, because I run many samples one time, I need to just use thread 1

hulai-hulai commented 2 years ago

这是来自QQ邮箱的假期自动回复邮件。   您好，我最近正在休假中，无法亲自回复您的邮件。我将在假期结束后，尽快给您回复。

asmlgkj commented 2 years ago

anyone has methods about this? thanks

tsy19900929 commented 1 year ago

other version solve this problem, https://github.com/tsy19900929/GeneFuse_Plus

hulai-hulai commented 1 year ago

这是来自QQ邮箱的假期自动回复邮件。   您好，我最近正在休假中，无法亲自回复您的邮件。我将在假期结束后，尽快给您回复。

lvzenglei commented 2 months ago

other version solve this problem, https://github.com/tsy19900929/GeneFuse_Plus

Hi, maybe, it can not solve the questions, just for my computer1-6, it run great on computer-2,and computer-4, however stuck on computer-[1,3,5,6],
1712908602504 trace log just stuck as below.

sudo strace -p 54952
strace: Process 54952 attached
strace: [ Process PID=54952 runs in x32 mode. ]

Any solutions? Thanks for that.

hulai-hulai commented 2 months ago

这是来自QQ邮箱的假期自动回复邮件。   您好，我最近正在休假中，无法亲自回复您的邮件。我将在假期结束后，尽快给您回复。

lvzenglei commented 2 months ago

other version solve this problem, https://github.com/tsy19900929/GeneFuse_Plus

Hi, maybe, it can not solve the questions, just for my computer1-6, it run great on computer-2,and computer-4, however stuck on computer-[1,3,5,6], 1712908602504 trace log just stuck as below.

sudo strace -p 54952
strace: Process 54952 attached
strace: [ Process PID=54952 runs in x32 mode. ]

Any solutions? Thanks for that.

sorry, It is ok, just my ref_file is wrong~~~ ,