I got data in bed.failed (orthologFind.py)

[vinitamehlawat]

Hi I ran HALPER manually following 4 steps shown in your repo https://github.com/pfenninglab/halLiftover-postprocessing/tree/master#running-steps-manually

After running all 4 steps I got 4 files with following extension:

1. .bed (Zero bytes)
2. .bed.failed (Both source genome and target genome bed coordinates with 9 columns)
3. .bed-peak.png
4. .bed.png

And both png also same (attached)

It would be very helpful if could you please help me to understand why I got the failed files have data but other one is zero bytes. What this .png is showing here

Thank you

[Yurun-Li-1024]

Hi, have you solve this problem?
I meet a similar problem. There was no ERROR report, but I got two empty output bed files (.bed and .bed.failed). Both png file are same with yours.
Could anyone help me for understanding this? Thanks a lot for any advice!

[imk1]

I am so sorry that I missed this for so long. My guess is that nothing in your outputs met the criteria for running HALPER. Can one of you send me your outputs from steps 1 and 3 as well as exactly what you ran for step 4?