[2020-04-26 02:22:38.177] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 02:22:38.178] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 02:22:38.178] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 02:22:38.178] [jointLog] [info] parsing read library format
[2020-04-26 02:22:38.178] [jointLog] [info] There is 1 library.
[2020-04-26 02:22:38.228] [jointLog] [info] Loading pufferfish index
[2020-04-26 02:22:38.228] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 02:22:38.401] [jointLog] [info] done
[2020-04-26 02:22:38.401] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 02:22:38.413] [jointLog] [info] Number of decoys : 0
[2020-04-26 02:22:44.969] [jointLog] [info] Computed 72,803 rich equivalence classes for further processing
[2020-04-26 02:22:44.969] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes 
[2020-04-26 02:22:44.986] [jointLog] [info] Number of mappings discarded because of alignment score : 461,137
[2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736
[2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352
[2020-04-26 02:22:44.989] [jointLog] [warning] Only 2278269 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 02:22:44.989] [jointLog] [info] Mapping rate = 99.1406%

[2020-04-26 02:22:44.989] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 02:22:44.991] [jointLog] [info] Starting optimizer
[2020-04-26 02:22:45.012] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 02:22:45.017] [jointLog] [info] iteration = 0 | max rel diff. = 5252.69
[2020-04-26 02:22:45.283] [jointLog] [info] iteration = 100 | max rel diff. = 3.94418
[2020-04-26 02:22:44.969] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-26 02:22:45.548] [jointLog] [info] iteration = 200 | max rel diff. = 0.477324
[2020-04-26 02:22:45.810] [jointLog] [info] iteration = 300 | max rel diff. = 0.25167
[2020-04-26 02:22:46.077] [jointLog] [info] iteration = 400 | max rel diff. = 0.108188
[2020-04-26 02:22:46.344] [jointLog] [info] iteration = 500 | max rel diff. = 0.0993165
[2020-04-26 02:22:46.609] [jointLog] [info] iteration = 600 | max rel diff. = 3.35828
[2020-04-26 02:22:46.878] [jointLog] [info] iteration = 700 | max rel diff. = 0.178284
[2020-04-26 02:22:47.154] [jointLog] [info] iteration = 800 | max rel diff. = 1.0699
[2020-04-26 02:22:47.265] [jointLog] [info] iteration = 841 | max rel diff. = 0.00762133
[2020-04-26 02:22:47.266] [jointLog] [info] Finished optimizer
[2020-04-26 02:22:47.266] [jointLog] [info] writing output