ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED

[Bharati Mehani]

Hi,

I am trying to use ROSE to identify super enhancers in H3K27Ac Chip-Seq data from a human cancer, but for few of my samples the command does not run successfully. After the bamToGFF conversion, the program waits for mapping and finally returns the following error:

ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED

I also tried to use more memory (64 and 100 GB) but it didn't help. Has anybody faced this issue before and can guide how to resolve this. I will really appreciate your help.

Thanks

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[夏夏]

Hello, I also encountered the same problem, how did you solve it？

[Pinpin Sui]

Hi， Have you find the reason for this error？

[Joey Zhong]

hello, if anyone still have this issue, you can try this:

change 144 to a bigger number, at line 443 of ROSE_main.py

        #CHANGE THIS PARAMETER TO ALLOW MORE TIME TO MAP
        if ticker == 144:
            print('ERROR: OPERATION TIME OUT. MAPPING OUTPUT NOT DETECTED')
            exit()
            break

‌

hope it helps