search

smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
66 stars 27 forks source link

MLML problems #144

Closed soleilll closed 4 years ago

soleilll commented 4 years ago

hello！ I have only two types of input are available,so i use them with the following command: mlml -u M7_RRBS.meth -m M7_oxRRBS.sort.meth -o test

but it said “mlml: mlml.cpp:509: int main(int, const char**): Assertion `f_chr == s_chr && f_pos == s_pos' failed.Aborted (core dumped)”

So would you please help me with these error？thank you very much！！！

terencewtli commented 4 years ago

Hi! Could you give us some guidance so we can reproduce the error? If you can find the line in the input files that give this error, that would be great. Running head -n 100 your_file on both input files might help too.

terencewtli commented 4 years ago

I've updated the code to throw a runtime error. Could you run it and show us the output?

terencewtli commented 4 years ago

Right now, we suspect that the files are not sorted the same way. Could you confirm that both files are sorted using the same locale? We generally use LC_ALL=C sort -o your_file_sorted your_file.

Soleilcode commented 4 years ago

@terencewtli Hi！ I'm sorry for the late reply. I have been delayed in some matters these days. I checked my files.I downloaded the test file and I generated a new file in the format of this file. Then sorted them with the code sort -k1,1 -k2,2n my_file. Finally,it works! But i forgot to filter my data with the coverage, so i got many 100% hmc. Anyway, it is another question. I have solved this mlml problem already. Thank you for your advise!!!

terencewtli commented 4 years ago

No problem! Glad it worked!!