Error running Shorah.py, and seeking for help

[JingniHe]

Hi, recently, I tried to use your tool " ShoRAH" to generate global reconstruction haplotypes, but I ran into some problems.

So I try to run the tool on Linux by using the command “./shorah.py -b sorted.bam -f ref.fa -w 48”. I generated the sorted bam file using BWA and SAMTOOLS, and the length of my read is 100.

At beginning, it would generate lots of files like this:

But then, it would run into an error showed as following:

It seems like something wrong with the codes, but I don't know how to fix this.

I sincerely hope for you suggestions and help. Thank you very much, and have a good day!

[DrYak]

Hello, could you please try with the empty_window branch mentionned in pull request #62 for issue #53 ?

(Or alternatively try the branch allocaholic ?)

We've fixed lots of bugs in these branches, perhaps it helps ?

[DrYak]

Small update, there's an alpha release which contains these fixes in the releases

It has successfully worked around lots of the bugs one of our user was having.

Among other it also fixes a bug which is triggered by dot in the file name. From the blurred error message you've posted, I think this is what is happening in your case.

If you do not want to use alpha code, you can circumvent this specific bug by renaming your sequence from K03455.1 to K034455_1.