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Error in if (sum(idx) == 0) { : missing value where TRUE/FALSE needed #8
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Hi Zhen, Thanks for opening an issue! If you could share a minimal example of code and subset of your data that reproduces this error, I can try to run it on my laptop and fix the problem. |
Please feel free to reopen this issue if you can provide a minimal example. |
Hey slowkow! I get the same error as Zhen. Here is the snippet of code and the corresponding error:
The code ran for couple of hours before throwing this error. So seems like something happened near the end of execution. I get the same error even if I remove the parameters "flank size" and/or "pval". Let me know if I can provide any more information or if you want me to open a new issue. Thanks! |
Hi Vatsal, thanks for sharing your code and error. That helps. If your session is still live, it would help if you run The error might come from this code (line 163): CENTIPEDE.tutorial/R/functions.R Lines 151 to 165 in 12811e7
If you can share data and code that I can run on laptop, then I might be able to help. Otherwise, I would suggest that you try running the code from Good luck! Let me know if you figure it out! |
Thanks for responding so quickly Kamil! I did run the traceback command. Here's the output:
I doubt this is very helpful for you. Since the input files are massive, would you like a trimmed down version of those files? I worry that these smaller files may disallow you to duplicate the exact error.
I still haven't tried this so will let you know if I find something interesting. |
So it turns out there was an issue with the BAM file. When I used the "deduped" BAM file, the problem seems to disappear. May be it is important for CENTIPEDE that the BAM file is without duplicates? I am not sure but at the moment that has fixed the issue. |
Hi all, I have the same problem. Thank you. Shoko |
Hi,
When I run the centipede_data , the result show :
Error in if (sum(idx) == 0) { : missing value where TRUE/FALSE needed.
Maybe it is some problem with my bam file?
Thanks
Zhen
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