complementBed error w/ genome file

[yaaminiv]

TL;DR complementBed doesn't like the format of my genome file and I'm not sure why

I'm using complementBed to generate a non-coding sequence track for the Roslin genome in this Jupyter notebook. Once I have a non-coding sequence track, I can create an intron track.

When I try running the complementBed code (pulled from my C. virginica notebook), I get the following error regarding my genome file:

I have the two required fields: chromosome and chromosome length, and (I believe) it's a tab-delimited file! I used the following code in my Jupyter notebook to create the file:

Do I need to reformat my file/generate it differently so complementBed recognizes the two fields?

[yaaminiv]

Realized bedtools v.2.17.0 was in my path, but I used v.2.26.0 in my previous code! I was able to switch to that version and run my code

[kubu4]

Whoa! Tricky! Nice troubleshooting!

How'd you catch the version differences?

[yaaminiv]

I looked at the directory I was calling with the {bedtoolsDirectory} variable in my previous notebook, and saw that it was different from the one in my path! So then I checked the versions.

[yaaminiv]

Update, I now have the same error with flankBed:

I want to create 1000 bp flanking regions for my gene track using the following code (pulled from this notebook):

I'm using flankBed v.2.26.0 and encountering this error, but I'm not encountering that error for complementBed anymore! So now I am confused.

[yaaminiv]

I ended up adding sed 's/Cr//g' after the awk code (take characters 2-14 of the header) to remove the remaining "Cr" in certain entries!

Still throws out the same error.

I'll try using the index file and report back.

[yaaminiv]

OKAY NEW PROBLEM. I think flankBed is angry because the first line in my file is blank...

[kubu4]

I'd agree. Is that from the FastA index?

[yaaminiv]

Yup, that was the issue! I had a weird empty first line in my file.

[yaaminiv]

Is that from the FastA index?

No! I didn't end up using the FastA index