[2020-04-26 11:46:30.112] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 11:46:30.112] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 11:46:30.112] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 11:46:30.112] [jointLog] [info] parsing read library format
[2020-04-26 11:46:30.112] [jointLog] [info] There is 1 library.
[2020-04-26 11:46:30.162] [jointLog] [info] Loading pufferfish index
[2020-04-26 11:46:30.162] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 11:46:30.461] [jointLog] [info] done
[2020-04-26 11:46:30.461] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 11:46:30.472] [jointLog] [info] Number of decoys : 0
[2020-04-26 11:46:37.097] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-26 11:46:37.097] [jointLog] [info] Computed 76,632 rich equivalence classes for further processing
[2020-04-26 11:46:37.097] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes 
[2020-04-26 11:46:37.113] [jointLog] [info] Number of mappings discarded because of alignment score : 536,822
[2020-04-26 11:46:37.113] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061
[2020-04-26 11:46:37.113] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 11:46:37.113] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328
[2020-04-26 11:46:37.117] [jointLog] [warning] Only 2319185 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 11:46:37.117] [jointLog] [info] Mapping rate = 99.1791%

[2020-04-26 11:46:37.117] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 11:46:37.119] [jointLog] [info] Starting optimizer
[2020-04-26 11:46:37.141] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 11:46:37.147] [jointLog] [info] iteration = 0 | max rel diff. = 4684.78
[2020-04-26 11:46:37.431] [jointLog] [info] iteration = 100 | max rel diff. = 4.42346
[2020-04-26 11:46:37.710] [jointLog] [info] iteration = 200 | max rel diff. = 1.50462
[2020-04-26 11:46:37.989] [jointLog] [info] iteration = 300 | max rel diff. = 0.45935
[2020-04-26 11:46:38.270] [jointLog] [info] iteration = 400 | max rel diff. = 0.0413828
[2020-04-26 11:46:38.548] [jointLog] [info] iteration = 500 | max rel diff. = 0.055984
[2020-04-26 11:46:38.827] [jointLog] [info] iteration = 600 | max rel diff. = 0.56642
[2020-04-26 11:46:39.108] [jointLog] [info] iteration = 700 | max rel diff. = 0.0272829
[2020-04-26 11:46:39.392] [jointLog] [info] iteration = 800 | max rel diff. = 0.414543
[2020-04-26 11:46:39.670] [jointLog] [info] iteration = 900 | max rel diff. = 2.30576
[2020-04-26 11:46:39.784] [jointLog] [info] iteration = 942 | max rel diff. = 0.00887826
[2020-04-26 11:46:39.785] [jointLog] [info] Finished optimizer
[2020-04-26 11:46:39.785] [jointLog] [info] writing output