Odd wombat behavior in squid

From Therese:

Here is the bed I was working with in wombat: 
/projectb/scratch/mitros/squid/doveOrder/wombat/PB_DBDOVE.chrname.bed.gz

genome 

/projectb/scratch/mitros/squid/doveOrder/dbdove_ord1.fa

here is the break that doesn't make sense in IGV:

chr17:636977-637304 BREAK

It is near gap 

chr17	637502	637602	gap13



wombat picked the following parameters:

[wombat] 2017-10-13 14:09:31,152 [INFO] WOMBAT v0.1.8
[wombat] 2017-10-13 14:09:31,152 [INFO] Python v2.7.10 (default, Nov 23 2015, 12:30:23)  [GCC 4.6.3]
[wombat] 2017-10-13 14:09:31,152 [INFO] Command: wombat -L chr17.list -l 999 PB_DBDOVE.chrname.bed.gz ../dbdove_ord1.fa limit999chr17
[wombat] 2017-10-13 14:09:31,300 [INFO] Inferring parameters:
[wombat] 2017-10-13 14:09:32,430 [INFO]   Inferring span window width and step sizes
[wombat] 2017-10-13 14:09:32,876 [INFO]   Estimating span threshold
[wombat] 2017-10-13 14:09:35,615 [WARNING]  Bad fit, estimating by integration
[wombat] 2017-10-13 14:09:35,615 [WARNING]  Estimated span threshold too low, defaulting to 4
[wombat] 2017-10-13 14:09:35,616 [INFO]   Inferring term window width and step sizes
[wombat] 2017-10-13 14:09:35,981 [INFO]   Estimating term threshold
[wombat] 2017-10-13 14:09:38,042 [INFO]   Inferred parameters:
[wombat] 2017-10-13 14:09:38,042 [INFO]     span-width: 656
[wombat] 2017-10-13 14:09:38,042 [INFO]     span-step:  328
[wombat] 2017-10-13 14:09:38,042 [INFO]     span-alpha: 0.01 (=4)
[wombat] 2017-10-13 14:09:38,042 [INFO]     term-width: 164
[wombat] 2017-10-13 14:09:38,042 [INFO]     term-step:  82
[wombat] 2017-10-13 14:09:38,042 [INFO]     term-alpha: 0.05 (=3)
[wombat] 2017-10-13 14:09:38,043 [INFO] Identifying reference breaks:
[wombat] 2017-10-13 14:09:39,131 [INFO]   Traversing chr17
[wombat] 2017-10-13 14:13:40,114 [INFO] Finished