[2020-04-26 10:17:15.877] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 10:17:15.877] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 10:17:15.877] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 10:17:15.877] [jointLog] [info] parsing read library format
[2020-04-26 10:17:15.877] [jointLog] [info] There is 1 library.
[2020-04-26 10:17:15.939] [jointLog] [info] Loading pufferfish index
[2020-04-26 10:17:15.939] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 10:17:16.123] [jointLog] [info] done
[2020-04-26 10:17:16.123] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 10:17:16.136] [jointLog] [info] Number of decoys : 0
[2020-04-26 10:17:18.890] [fileLog] [info] 
At end of round 0
==================
Observed 815223 total fragments (815223 in most recent round)

[2020-04-26 10:17:18.889] [jointLog] [info] Computed 61,276 rich equivalence classes for further processing
[2020-04-26 10:17:18.889] [jointLog] [info] Counted 792,535 total reads in the equivalence classes 
[2020-04-26 10:17:18.905] [jointLog] [info] Number of mappings discarded because of alignment score : 329,164
[2020-04-26 10:17:18.905] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,416
[2020-04-26 10:17:18.905] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 10:17:18.905] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,914
[2020-04-26 10:17:18.909] [jointLog] [warning] Only 792535 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 10:17:18.909] [jointLog] [info] Mapping rate = 97.217%

[2020-04-26 10:17:18.909] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 10:17:18.911] [jointLog] [info] Starting optimizer
[2020-04-26 10:17:18.935] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 10:17:18.939] [jointLog] [info] iteration = 0 | max rel diff. = 1898.46
[2020-04-26 10:17:19.174] [jointLog] [info] iteration = 100 | max rel diff. = 5.35679
[2020-04-26 10:17:19.406] [jointLog] [info] iteration = 200 | max rel diff. = 1.21457
[2020-04-26 10:17:19.635] [jointLog] [info] iteration = 300 | max rel diff. = 0.0169194
[2020-04-26 10:17:19.865] [jointLog] [info] iteration = 400 | max rel diff. = 0.00502364
[2020-04-26 10:17:19.865] [jointLog] [info] iteration = 401 | max rel diff. = 0.00502364
[2020-04-26 10:17:19.866] [jointLog] [info] Finished optimizer
[2020-04-26 10:17:19.866] [jointLog] [info] writing output