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gphocs-dev / G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.
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Can't load trace files #63

Closed btmartin721 closed 5 years ago

btmartin721 commented 5 years ago

Hello,

I am trying to load my trace files into Tracer and readTrace, and neither will work. I have attached one of my trace files.

If I try to run readTrace, I get the following error:

Unable to count lines of the trace file

When I try to import it into Tracer, the program acts like it loads it but nothing happens. Nothing gets loaded.

Do you know what could be wrong? This is from a file that has not finished running yet, but I am trying to view the traces while it's still running (though the file is a copy, not the one being written to).

-Bradley

box_gphocs_r1.log

gphocs-dev commented 5 years ago

Dear Martin,

The trace file looks completely fine to me. I was able to open it without a problem using Tracer v1.5. I know from other user posts that the latest version of Tracer sometimes does not work. We'll have to look into that to see what's causing this. I also notice now that there is a minor bug in our readTrace program that prevents it from correctly reading trace files. We'll add this to our bug list and fix it soon.

Sorry for the inconvenience.

--Ilan

btmartin721 commented 5 years ago

Thank you for your help. I'll give an older version of Tracer a try. If I don't have success I'll let you know.

Also, I might have figured something out with the readTrace. Apparently G-Phocs puts an \r\n as the carriage return, whereas it should just be the Linux newline \n. I was using the latest dev version of G-Phocs (1.3).

So I removed the \r and it ran through readTrace. Not sure if it added the \r because of something I did or if it was just part of the code. I was running it on a Linux cluster (running CentOS 6).

-Bradley

btmartin721 commented 5 years ago

Yes, Tracer v1.6 worked. Thanks again for your help.

-Bradley

gphocs-dev commented 5 years ago

As far as I can tell, the code is not explicitly writing \r characters into the trace files, so that is a bit odd. We'll have a look to see if there is some odd conversion issue involved. Anyway, I'm glad to see that it works out for you.