[2020-04-06 17:31:52.889] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-06 17:31:52.889] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-06 17:31:52.889] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-06 17:31:52.889] [jointLog] [info] parsing read library format
[2020-04-06 17:31:52.889] [jointLog] [info] There is 1 library.
[2020-04-06 17:31:52.953] [jointLog] [info] Loading pufferfish index
[2020-04-06 17:31:52.953] [jointLog] [info] Loading dense pufferfish index.
[2020-04-06 17:31:52.972] [jointLog] [info] done
[2020-04-06 17:31:52.972] [jointLog] [info] Index contained 5,183 targets
[2020-04-06 17:31:52.975] [jointLog] [info] Number of decoys : 0
[2020-04-06 17:31:55.123] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.245] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:31:55.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.268] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.271] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.278] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2020-04-06 17:31:55.288] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.302] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.305] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.305] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.306] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.314] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.317] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.327] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.329] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.334] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.339] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.340] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.343] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments
[2020-04-06 17:31:55.346] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.347] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments
[2020-04-06 17:31:55.590] [jointLog] [info] Computed 9,130 rich equivalence classes for further processing
[2020-04-06 17:31:55.590] [jointLog] [info] Counted 639,747 total reads in the equivalence classes 
[2020-04-06 17:31:55.603] [jointLog] [info] Number of mappings discarded because of alignment score : 27,472
[2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,748
[2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 23
[2020-04-06 17:31:55.604] [jointLog] [warning] Only 639747 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-06 17:31:55.604] [jointLog] [info] Mapping rate = 98.8296%

[2020-04-06 17:31:55.604] [jointLog] [info] finished quantifyLibrary()
[2020-04-06 17:31:55.605] [jointLog] [info] Starting optimizer
[2020-04-06 17:31:55.611] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-06 17:31:55.612] [jointLog] [info] iteration = 0 | max rel diff. = 11003.1
[2020-04-06 17:31:55.645] [jointLog] [info] iteration = 100 | max rel diff. = 0.270096
[2020-04-06 17:31:55.674] [jointLog] [info] iteration = 200 | max rel diff. = 0.80245
[2020-04-06 17:31:55.701] [jointLog] [info] iteration = 300 | max rel diff. = 0.0157792
[2020-04-06 17:31:55.727] [jointLog] [info] iteration = 400 | max rel diff. = 0.0982042
[2020-04-06 17:31:55.751] [jointLog] [info] iteration = 500 | max rel diff. = 0.0321339
[2020-04-06 17:31:55.770] [jointLog] [info] iteration = 584 | max rel diff. = 0.00078143
[2020-04-06 17:31:55.770] [jointLog] [info] Finished optimizer
[2020-04-06 17:31:55.770] [jointLog] [info] writing output 

[2020-04-06 17:31:55.591] [fileLog] [info] 
At end of round 0
==================
Observed 647323 total fragments (647323 in most recent round)