[2020-04-26 00:09:56.066] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 00:09:56.066] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 00:09:56.066] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 00:09:56.066] [jointLog] [info] parsing read library format
[2020-04-26 00:09:56.066] [jointLog] [info] There is 1 library.
[2020-04-26 00:09:56.119] [jointLog] [info] Loading pufferfish index
[2020-04-26 00:09:56.119] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 00:09:56.195] [jointLog] [info] done
[2020-04-26 00:09:56.195] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 00:09:56.207] [jointLog] [info] Number of decoys : 0
[2020-04-26 00:10:01.918] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-26 00:10:01.918] [jointLog] [info] Computed 81,772 rich equivalence classes for further processing
[2020-04-26 00:10:01.918] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes 
[2020-04-26 00:10:01.940] [jointLog] [info] Number of mappings discarded because of alignment score : 733,448
[2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154
[2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582
[2020-04-26 00:10:01.943] [jointLog] [warning] Only 1745454 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 00:10:01.943] [jointLog] [info] Mapping rate = 98.6937%

[2020-04-26 00:10:01.943] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 00:10:01.945] [jointLog] [info] Starting optimizer
[2020-04-26 00:10:01.967] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 00:10:01.974] [jointLog] [info] iteration = 0 | max rel diff. = 3747.53
[2020-04-26 00:10:02.335] [jointLog] [info] iteration = 100 | max rel diff. = 4.41432
[2020-04-26 00:10:02.693] [jointLog] [info] iteration = 200 | max rel diff. = 5.26484
[2020-04-26 00:10:03.050] [jointLog] [info] iteration = 300 | max rel diff. = 1.30696
[2020-04-26 00:10:03.408] [jointLog] [info] iteration = 400 | max rel diff. = 0.0219816
[2020-04-26 00:10:03.766] [jointLog] [info] iteration = 500 | max rel diff. = 0.0962094
[2020-04-26 00:10:04.125] [jointLog] [info] iteration = 600 | max rel diff. = 0.488996
[2020-04-26 00:10:04.136] [jointLog] [info] iteration = 604 | max rel diff. = 0.00683818
[2020-04-26 00:10:04.137] [jointLog] [info] Finished optimizer
[2020-04-26 00:10:04.137] [jointLog] [info] writing output