[2020-04-26 09:59:59.072] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:59:59.072] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:59:59.072] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:59:59.072] [jointLog] [info] parsing read library format
[2020-04-26 09:59:59.072] [jointLog] [info] There is 1 library.
[2020-04-26 09:59:59.124] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:59:59.124] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:59:59.302] [jointLog] [info] done
[2020-04-26 09:59:59.302] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:59:59.316] [jointLog] [info] Number of decoys : 0
[2020-04-26 10:00:09.579] [fileLog] [info] 
At end of round 0
==================
Observed 3213886 total fragments (3213886 in most recent round)

[2020-04-26 10:00:09.578] [jointLog] [info] Computed 93,716 rich equivalence classes for further processing
[2020-04-26 10:00:09.578] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes 
[2020-04-26 10:00:09.599] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,423
[2020-04-26 10:00:09.599] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413
[2020-04-26 10:00:09.599] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 10:00:09.599] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312
[2020-04-26 10:00:09.603] [jointLog] [warning] Only 3186382 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 10:00:09.603] [jointLog] [info] Mapping rate = 99.1442%

[2020-04-26 10:00:09.603] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 10:00:09.604] [jointLog] [info] Starting optimizer
[2020-04-26 10:00:09.630] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 10:00:09.639] [jointLog] [info] iteration = 0 | max rel diff. = 7295.18
[2020-04-26 10:00:10.102] [jointLog] [info] iteration = 100 | max rel diff. = 15.5799
[2020-04-26 10:00:10.562] [jointLog] [info] iteration = 200 | max rel diff. = 0.255845
[2020-04-26 10:00:11.015] [jointLog] [info] iteration = 300 | max rel diff. = 0.329047
[2020-04-26 10:00:11.471] [jointLog] [info] iteration = 400 | max rel diff. = 0.400591
[2020-04-26 10:00:11.927] [jointLog] [info] iteration = 500 | max rel diff. = 0.205394
[2020-04-26 10:00:12.111] [jointLog] [info] iteration = 540 | max rel diff. = 0.00668698
[2020-04-26 10:00:12.112] [jointLog] [info] Finished optimizer
[2020-04-26 10:00:12.112] [jointLog] [info] writing output