HapTree V1.0 (http://cb.csail.mit.edu/cb/haptree/) accepts as an argument, a fragment file.

From the README:

we use the same format as HapCut. At this time we recommend using HapCut's extracthairs to translate from BAM to fragment file.

I downloaded HapCUT2 and a deprecated version of HapCUT (last modified in 2014).

The problem is (I think), both versions of HapCUT produce the same fragment file ( https://imgur.com/LzxnxOG ), which is NOT consistent with the example fragment file from HapTree (https://imgur.com/3u6JvFl)

I've tested the HapCUT files with their respective versions of HapCUT and found that in both cases, phased haplotype blocks are assembled from the reads (which is the primary function of HapCUT) produced by HapCUT's extracthairs program which creates the fragment files.

Here is the error that HapTree throws when I try to execute the program: https://imgur.com/244HtyO

Does anyone with experience working with HapTree have any idea how to help? Thank you!