[2020-04-25 20:13:19.341] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-25 20:13:19.341] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-25 20:13:19.341] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-25 20:13:19.341] [jointLog] [info] parsing read library format
[2020-04-25 20:13:19.341] [jointLog] [info] There is 1 library.
[2020-04-25 20:13:19.393] [jointLog] [info] Loading pufferfish index
[2020-04-25 20:13:19.393] [jointLog] [info] Loading dense pufferfish index.
[2020-04-25 20:13:19.986] [jointLog] [info] done
[2020-04-25 20:13:19.986] [jointLog] [info] Index contained 40,435 targets
[2020-04-25 20:13:20.011] [jointLog] [info] Number of decoys : 0
[2020-04-25 20:13:26.499] [fileLog] [info] 
At end of round 0
==================
Observed 2298019 total fragments (2298019 in most recent round)

[2020-04-25 20:13:26.499] [jointLog] [info] Computed 73,208 rich equivalence classes for further processing
[2020-04-25 20:13:26.499] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes 
[2020-04-25 20:13:26.515] [jointLog] [info] Number of mappings discarded because of alignment score : 461,132
[2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736
[2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,351
[2020-04-25 20:13:26.518] [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.

[2020-04-25 20:13:26.518] [jointLog] [info] Mapping rate = 99.1406%

[2020-04-25 20:13:26.518] [jointLog] [info] finished quantifyLibrary()
[2020-04-25 20:13:26.520] [jointLog] [info] Starting optimizer
[2020-04-25 20:13:26.543] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-25 20:13:26.548] [jointLog] [info] iteration = 0 | max rel diff. = 5253.15
[2020-04-25 20:13:26.832] [jointLog] [info] iteration = 100 | max rel diff. = 3.44095
[2020-04-25 20:13:27.107] [jointLog] [info] iteration = 200 | max rel diff. = 13.1233
[2020-04-25 20:13:27.379] [jointLog] [info] iteration = 300 | max rel diff. = 0.347319
[2020-04-25 20:13:27.650] [jointLog] [info] iteration = 400 | max rel diff. = 0.107838
[2020-04-25 20:13:27.924] [jointLog] [info] iteration = 500 | max rel diff. = 3.50026
[2020-04-25 20:13:28.202] [jointLog] [info] iteration = 600 | max rel diff. = 0.130658
[2020-04-25 20:13:28.482] [jointLog] [info] iteration = 700 | max rel diff. = 0.0500265
[2020-04-25 20:13:28.757] [jointLog] [info] iteration = 800 | max rel diff. = 0.0270105
[2020-04-25 20:13:28.942] [jointLog] [info] iteration = 868 | max rel diff. = 0.00943807
[2020-04-25 20:13:28.944] [jointLog] [info] Finished optimizer
[2020-04-25 20:13:28.944] [jointLog] [info] writing output