[2020-04-26 13:21:24.704] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 13:21:24.704] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 13:21:24.704] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 13:21:24.704] [jointLog] [info] parsing read library format
[2020-04-26 13:21:24.704] [jointLog] [info] There is 1 library.
[2020-04-26 13:21:24.769] [jointLog] [info] Loading pufferfish index
[2020-04-26 13:21:24.769] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 13:21:24.850] [jointLog] [info] done
[2020-04-26 13:21:24.850] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 13:21:24.863] [jointLog] [info] Number of decoys : 0
[2020-04-26 13:21:32.146] [fileLog] [info] 
At end of round 0
==================
Observed 2563755 total fragments (2563755 in most recent round)

[2020-04-26 13:21:32.145] [jointLog] [info] Computed 81,224 rich equivalence classes for further processing
[2020-04-26 13:21:32.145] [jointLog] [info] Counted 2,537,571 total reads in the equivalence classes 
[2020-04-26 13:21:32.167] [jointLog] [info] Number of mappings discarded because of alignment score : 763,751
[2020-04-26 13:21:32.167] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,277
[2020-04-26 13:21:32.167] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 13:21:32.167] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111
[2020-04-26 13:21:32.171] [jointLog] [warning] Only 2537571 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 13:21:32.171] [jointLog] [info] Mapping rate = 98.9787%

[2020-04-26 13:21:32.171] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 13:21:32.172] [jointLog] [info] Starting optimizer
[2020-04-26 13:21:32.195] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 13:21:32.201] [jointLog] [info] iteration = 0 | max rel diff. = 5796.58
[2020-04-26 13:21:32.520] [jointLog] [info] iteration = 100 | max rel diff. = 20.513
[2020-04-26 13:21:32.835] [jointLog] [info] iteration = 200 | max rel diff. = 2.41013
[2020-04-26 13:21:33.154] [jointLog] [info] iteration = 300 | max rel diff. = 0.56036
[2020-04-26 13:21:33.467] [jointLog] [info] iteration = 400 | max rel diff. = 0.0563118
[2020-04-26 13:21:33.786] [jointLog] [info] iteration = 500 | max rel diff. = 2.02166
[2020-04-26 13:21:34.106] [jointLog] [info] iteration = 600 | max rel diff. = 0.104365
[2020-04-26 13:21:34.423] [jointLog] [info] iteration = 700 | max rel diff. = 0.0821437
[2020-04-26 13:21:34.739] [jointLog] [info] iteration = 800 | max rel diff. = 0.0186174
[2020-04-26 13:21:35.058] [jointLog] [info] iteration = 900 | max rel diff. = 0.0771548
[2020-04-26 13:21:35.382] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0114546
[2020-04-26 13:21:35.701] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0400682
[2020-04-26 13:21:35.884] [jointLog] [info] iteration = 1,158 | max rel diff. = 0.00807113
[2020-04-26 13:21:35.888] [jointLog] [info] Finished optimizer
[2020-04-26 13:21:35.888] [jointLog] [info] writing output