[2020-04-26 12:12:34.657] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 12:12:34.657] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 12:12:34.657] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 12:12:34.657] [jointLog] [info] parsing read library format
[2020-04-26 12:12:34.657] [jointLog] [info] There is 1 library.
[2020-04-26 12:12:34.722] [jointLog] [info] Loading pufferfish index
[2020-04-26 12:12:34.722] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 12:12:34.870] [jointLog] [info] done
[2020-04-26 12:12:34.870] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 12:12:34.884] [jointLog] [info] Number of decoys : 0
[2020-04-26 12:12:43.539] [jointLog] [info] Computed 79,675 rich equivalence classes for further processing
[2020-04-26 12:12:43.539] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes 
[2020-04-26 12:12:43.561] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,006
[2020-04-26 12:12:43.561] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705
[2020-04-26 12:12:43.561] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 12:12:43.561] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808
[2020-04-26 12:12:43.565] [jointLog] [warning] Only 2609007 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-26 12:12:43.565] [jointLog] [info] Mapping rate = 99.1136%

[2020-04-26 12:12:43.565] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 12:12:43.566] [jointLog] [info] Starting optimizer
[2020-04-26 12:12:43.594] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 12:12:43.603] [jointLog] [info] iteration = 0 | max rel diff. = 6032.76
[2020-04-26 12:12:43.539] [fileLog] [info] 
At end of round 0
==================
Observed 2632340 total fragments (2632340 in most recent round)

[2020-04-26 12:12:44.003] [jointLog] [info] iteration = 100 | max rel diff. = 8.70001
[2020-04-26 12:12:44.395] [jointLog] [info] iteration = 200 | max rel diff. = 14.6458
[2020-04-26 12:12:44.794] [jointLog] [info] iteration = 300 | max rel diff. = 0.22391
[2020-04-26 12:12:45.190] [jointLog] [info] iteration = 400 | max rel diff. = 0.0935759
[2020-04-26 12:12:45.587] [jointLog] [info] iteration = 500 | max rel diff. = 0.0843977
[2020-04-26 12:12:45.638] [jointLog] [info] iteration = 514 | max rel diff. = 0.00590091
[2020-04-26 12:12:45.642] [jointLog] [info] Finished optimizer
[2020-04-26 12:12:45.642] [jointLog] [info] writing output