[2020-04-26 07:30:38.052] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 07:30:38.052] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 07:30:38.052] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 07:30:38.052] [jointLog] [info] parsing read library format
[2020-04-26 07:30:38.052] [jointLog] [info] There is 1 library.
[2020-04-26 07:30:38.107] [jointLog] [info] Loading pufferfish index
[2020-04-26 07:30:38.107] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 07:30:38.225] [jointLog] [info] done
[2020-04-26 07:30:38.225] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 07:30:38.236] [jointLog] [info] Number of decoys : 0
[2020-04-26 07:30:46.586] [fileLog] [info] 
At end of round 0
==================
Observed 2632340 total fragments (2632340 in most recent round)

[2020-04-26 07:30:46.585] [jointLog] [info] Computed 79,760 rich equivalence classes for further processing
[2020-04-26 07:30:46.585] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes 
[2020-04-26 07:30:46.606] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,006
[2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705
[2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808
[2020-04-26 07:30:46.609] [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 07:30:46.609] [jointLog] [info] Mapping rate = 99.1136%

[2020-04-26 07:30:46.609] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 07:30:46.610] [jointLog] [info] Starting optimizer
[2020-04-26 07:30:46.632] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 07:30:46.641] [jointLog] [info] iteration = 0 | max rel diff. = 6035.68
[2020-04-26 07:30:47.039] [jointLog] [info] iteration = 100 | max rel diff. = 6.73724
[2020-04-26 07:30:47.426] [jointLog] [info] iteration = 200 | max rel diff. = 9.10024
[2020-04-26 07:30:47.816] [jointLog] [info] iteration = 300 | max rel diff. = 0.222748
[2020-04-26 07:30:48.101] [jointLog] [info] iteration = 375 | max rel diff. = 0.00742665
[2020-04-26 07:30:48.102] [jointLog] [info] Finished optimizer
[2020-04-26 07:30:48.102] [jointLog] [info] writing output