[2020-04-25 23:05:54.416] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 23:05:54.416] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 23:05:54.416] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 23:05:54.416] [jointLog] [info] parsing read library format
[2020-04-25 23:05:54.416] [jointLog] [info] There is 1 library.
[2020-04-25 23:05:54.474] [jointLog] [info] Loading pufferfish index
[2020-04-25 23:05:54.474] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 23:05:54.556] [jointLog] [info] done
[2020-04-25 23:05:54.556] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 23:05:54.570] [jointLog] [info] Number of decoys : 0
[2020-04-25 23:05:58.695] [jointLog] [info] Computed 70,045 rich equivalence classes for further processing
[2020-04-25 23:05:58.695] [jointLog] [info] Counted 1,295,949 total reads in the equivalence classes 
[2020-04-25 23:05:58.712] [jointLog] [info] Number of mappings discarded because of alignment score : 406,726
[2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,982
[2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002
[2020-04-25 23:05:58.716] [jointLog] [warning] Only 1295949 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-25 23:05:58.716] [jointLog] [info] Mapping rate = 98.1522%

[2020-04-25 23:05:58.716] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 23:05:58.718] [jointLog] [info] Starting optimizer
[2020-04-25 23:05:58.738] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 23:05:58.742] [jointLog] [info] iteration = 0 | max rel diff. = 3061.97
[2020-04-25 23:05:58.696] [fileLog] [info] 
At end of round 0
==================
Observed 1320346 total fragments (1320346 in most recent round)

[2020-04-25 23:05:58.984] [jointLog] [info] iteration = 100 | max rel diff. = 8.23365
[2020-04-25 23:05:59.229] [jointLog] [info] iteration = 200 | max rel diff. = 2.37361
[2020-04-25 23:05:59.471] [jointLog] [info] iteration = 300 | max rel diff. = 0.160402
[2020-04-25 23:05:59.705] [jointLog] [info] iteration = 400 | max rel diff. = 2.00434
[2020-04-25 23:05:59.940] [jointLog] [info] iteration = 500 | max rel diff. = 0.12409
[2020-04-25 23:06:00.180] [jointLog] [info] iteration = 600 | max rel diff. = 0.0371456
[2020-04-25 23:06:00.417] [jointLog] [info] iteration = 700 | max rel diff. = 0.0181668
[2020-04-25 23:06:00.542] [jointLog] [info] iteration = 752 | max rel diff. = 0.00805883
[2020-04-25 23:06:00.543] [jointLog] [info] Finished optimizer
[2020-04-25 23:06:00.543] [jointLog] [info] writing output