[2020-04-26 08:39:29.377] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 08:39:29.377] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 08:39:29.377] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 08:39:29.377] [jointLog] [info] parsing read library format
[2020-04-26 08:39:29.377] [jointLog] [info] There is 1 library.
[2020-04-26 08:39:29.435] [jointLog] [info] Loading pufferfish index
[2020-04-26 08:39:29.435] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 08:39:29.517] [jointLog] [info] done
[2020-04-26 08:39:29.517] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 08:39:29.530] [jointLog] [info] Number of decoys : 0
[2020-04-26 08:39:36.988] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-26 08:39:36.987] [jointLog] [info] Computed 81,283 rich equivalence classes for further processing
[2020-04-26 08:39:36.987] [jointLog] [info] Counted 2,537,570 total reads in the equivalence classes 
[2020-04-26 08:39:37.011] [jointLog] [info] Number of mappings discarded because of alignment score : 763,753
[2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,278
[2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111
[2020-04-26 08:39:37.015] [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 08:39:37.015] [jointLog] [info] Mapping rate = 98.9786%

[2020-04-26 08:39:37.015] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 08:39:37.017] [jointLog] [info] Starting optimizer
[2020-04-26 08:39:37.040] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 08:39:37.046] [jointLog] [info] iteration = 0 | max rel diff. = 5794.47
[2020-04-26 08:39:37.370] [jointLog] [info] iteration = 100 | max rel diff. = 20.9384
[2020-04-26 08:39:37.694] [jointLog] [info] iteration = 200 | max rel diff. = 2.32699
[2020-04-26 08:39:38.013] [jointLog] [info] iteration = 300 | max rel diff. = 14.1017
[2020-04-26 08:39:38.332] [jointLog] [info] iteration = 400 | max rel diff. = 0.074888
[2020-04-26 08:39:38.661] [jointLog] [info] iteration = 500 | max rel diff. = 1.13821
[2020-04-26 08:39:38.968] [jointLog] [info] iteration = 596 | max rel diff. = 0.00983689
[2020-04-26 08:39:38.969] [jointLog] [info] Finished optimizer
[2020-04-26 08:39:38.969] [jointLog] [info] writing output