[2020-04-26 04:34:58.783] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 04:34:58.783] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 04:34:58.783] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 04:34:58.783] [jointLog] [info] parsing read library format
[2020-04-26 04:34:58.783] [jointLog] [info] There is 1 library.
[2020-04-26 04:34:58.843] [jointLog] [info] Loading pufferfish index
[2020-04-26 04:34:58.843] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 04:34:59.024] [jointLog] [info] done
[2020-04-26 04:34:59.024] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 04:34:59.038] [jointLog] [info] Number of decoys : 0
[2020-04-26 04:35:07.430] [fileLog] [info] 
At end of round 0
==================
Observed 2632340 total fragments (2632340 in most recent round)

[2020-04-26 04:35:07.430] [jointLog] [info] Computed 79,691 rich equivalence classes for further processing
[2020-04-26 04:35:07.430] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes 
[2020-04-26 04:35:07.451] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,009
[2020-04-26 04:35:07.451] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705
[2020-04-26 04:35:07.451] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 04:35:07.451] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808
[2020-04-26 04:35:07.456] [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 04:35:07.456] [jointLog] [info] Mapping rate = 99.1136%

[2020-04-26 04:35:07.456] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 04:35:07.457] [jointLog] [info] Starting optimizer
[2020-04-26 04:35:07.478] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 04:35:07.486] [jointLog] [info] iteration = 0 | max rel diff. = 6035.12
[2020-04-26 04:35:07.885] [jointLog] [info] iteration = 100 | max rel diff. = 10.043
[2020-04-26 04:35:08.276] [jointLog] [info] iteration = 200 | max rel diff. = 3.35315
[2020-04-26 04:35:08.662] [jointLog] [info] iteration = 300 | max rel diff. = 0.2209
[2020-04-26 04:35:08.947] [jointLog] [info] iteration = 374 | max rel diff. = 0.00735555
[2020-04-26 04:35:08.948] [jointLog] [info] Finished optimizer
[2020-04-26 04:35:08.948] [jointLog] [info] writing output