[2020-04-26 06:09:40.963] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 06:09:40.963] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 06:09:40.963] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 06:09:40.963] [jointLog] [info] parsing read library format
[2020-04-26 06:09:40.963] [jointLog] [info] There is 1 library.
[2020-04-26 06:09:41.022] [jointLog] [info] Loading pufferfish index
[2020-04-26 06:09:41.022] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 06:09:41.158] [jointLog] [info] done
[2020-04-26 06:09:41.158] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 06:09:41.170] [jointLog] [info] Number of decoys : 0
[2020-04-26 06:09:48.731] [jointLog] [info] Computed 81,299 rich equivalence classes for further processing
[2020-04-26 06:09:48.731] [jointLog] [info] Counted 2,537,570 total reads in the equivalence classes 
[2020-04-26 06:09:48.750] [jointLog] [info] Number of mappings discarded because of alignment score : 763,757
[2020-04-26 06:09:48.750] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,278
[2020-04-26 06:09:48.750] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 06:09:48.750] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111
[2020-04-26 06:09:48.754] [jointLog] [warning] Only 2537570 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 06:09:48.754] [jointLog] [info] Mapping rate = 98.9786%

[2020-04-26 06:09:48.754] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 06:09:48.755] [jointLog] [info] Starting optimizer
[2020-04-26 06:09:48.780] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 06:09:48.787] [jointLog] [info] iteration = 0 | max rel diff. = 5796.24
[2020-04-26 06:09:48.732] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-26 06:09:49.111] [jointLog] [info] iteration = 100 | max rel diff. = 7.88136
[2020-04-26 06:09:49.438] [jointLog] [info] iteration = 200 | max rel diff. = 2.363
[2020-04-26 06:09:49.753] [jointLog] [info] iteration = 300 | max rel diff. = 0.651894
[2020-04-26 06:09:50.069] [jointLog] [info] iteration = 400 | max rel diff. = 0.115653
[2020-04-26 06:09:50.386] [jointLog] [info] iteration = 500 | max rel diff. = 0.542573
[2020-04-26 06:09:50.707] [jointLog] [info] iteration = 600 | max rel diff. = 0.143495
[2020-04-26 06:09:51.034] [jointLog] [info] iteration = 700 | max rel diff. = 0.0546104
[2020-04-26 06:09:51.346] [jointLog] [info] iteration = 800 | max rel diff. = 0.0103413
[2020-04-26 06:09:51.664] [jointLog] [info] iteration = 900 | max rel diff. = 0.232381
[2020-04-26 06:09:51.979] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.588113
[2020-04-26 06:09:52.297] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.399636
[2020-04-26 06:09:52.418] [jointLog] [info] iteration = 1,139 | max rel diff. = 0.00173864
[2020-04-26 06:09:52.420] [jointLog] [info] Finished optimizer
[2020-04-26 06:09:52.420] [jointLog] [info] writing output