Problems with custome genomes

[GiuliaGuiducci]

Hi,
first of all thanks for creating such a great tool!

I am trying to run epic2 on my bam files aligned to h38. I have input chromosome sizes for h38 found on your github page and one of the -egf found always on your page. I am getting a huge error (I attach it here). I tried to filter my bam file to keep only the reads belonging to the chromosomes on the list, but didn't change much.

Could you help me in understanding the issue? Also, in line with other posts here, it is not clear which -egf we should use, as there are several ones on your github page.

Thanks in advance
Cheers

Giulia

Epic2_SMARCC1.e5619494.txt

[DavideBrex]

Hi Giulia, I am not the developer but I noticed that at the end of the error message there is IsADirectoryError: [Errno 21] Is a directory:.

Could you share the command you run please?

[GiuliaGuiducci]

Hello Davide,
I have run default options + the --chromsize and -egf, that I am not writing here.

${out} is the output folder
${Sample_filt} is the treatment bam file
${igg} is the control bam file

epic2 -t ${Sample_filt} -c ${igg} -m 2 --keep-duplicates -fdr 0.01 -o ${out}

Do you think that such a big error might be due to the output option?

[DavideBrex]

I believe the error is in line 337 (here) when the program tries to open the connection to the output file but instead receives a folder.

Try to provide as output a file and not a folder and it should run

[GiuliaGuiducci]

You are right! It worked! Thank you!