[2020-02-06 18:48:58.000] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-02-06 18:48:58.000] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-02-06 18:48:58.000] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-02-06 18:48:58.000] [jointLog] [info] parsing read library format
[2020-02-06 18:48:58.000] [jointLog] [info] There is 1 library.
[2020-02-06 18:48:58.066] [jointLog] [info] Loading pufferfish index
[2020-02-06 18:48:58.066] [jointLog] [info] Loading dense pufferfish index.
[2020-02-06 18:48:58.464] [jointLog] [info] done
[2020-02-06 18:48:58.464] [jointLog] [info] Index contained 19,670 targets
[2020-02-06 18:48:58.479] [jointLog] [info] Number of decoys : 0
[2020-02-06 18:49:15.594] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.595] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.604] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.620] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.621] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.624] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments
[2020-02-06 18:49:15.626] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.634] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.637] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.640] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:49:15.642] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.645] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:49:15.653] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.671] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.673] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.679] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.682] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.683] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.685] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:49:15.687] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.689] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments
[2020-02-06 18:49:15.693] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.694] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.703] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments
[2020-02-06 18:49:15.704] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2020-02-06 18:49:15.706] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.708] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments
[2020-02-06 18:49:15.711] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2020-02-06 18:49:15.869] [jointLog] [info] Computed 46,371 rich equivalence classes for further processing
[2020-02-06 18:49:15.869] [jointLog] [info] Counted 6,295,915 total reads in the equivalence classes 
[2020-02-06 18:49:15.881] [jointLog] [info] Number of mappings discarded because of alignment score : 723,429
[2020-02-06 18:49:15.881] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,703
[2020-02-06 18:49:15.881] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-02-06 18:49:15.881] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,423
[2020-02-06 18:49:15.881] [jointLog] [info] Mapping rate = 99.5524%

[2020-02-06 18:49:15.881] [jointLog] [info] finished quantifyLibrary()
[2020-02-06 18:49:15.883] [jointLog] [info] Starting optimizer
[2020-02-06 18:49:15.895] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-02-06 18:49:15.898] [jointLog] [info] iteration = 0 | max rel diff. = 26955.4
[2020-02-06 18:49:16.085] [jointLog] [info] iteration = 100 | max rel diff. = 6.18189
[2020-02-06 18:49:15.869] [fileLog] [info] 
At end of round 0
==================
Observed 6324223 total fragments (6324223 in most recent round)

[2020-02-06 18:49:16.239] [jointLog] [info] iteration = 200 | max rel diff. = 8.5154
[2020-02-06 18:49:16.393] [jointLog] [info] iteration = 300 | max rel diff. = 0.164255
[2020-02-06 18:49:16.548] [jointLog] [info] iteration = 400 | max rel diff. = 18.7107
[2020-02-06 18:49:16.701] [jointLog] [info] iteration = 500 | max rel diff. = 0.0494179
[2020-02-06 18:49:16.855] [jointLog] [info] iteration = 600 | max rel diff. = 0.0400209
[2020-02-06 18:49:17.008] [jointLog] [info] iteration = 700 | max rel diff. = 0.0390763
[2020-02-06 18:49:17.161] [jointLog] [info] iteration = 800 | max rel diff. = 0.0240937
[2020-02-06 18:49:17.315] [jointLog] [info] iteration = 900 | max rel diff. = 0.00861202
[2020-02-06 18:49:17.315] [jointLog] [info] iteration = 901 | max rel diff. = 0.00861202
[2020-02-06 18:49:17.315] [jointLog] [info] Finished optimizer
[2020-02-06 18:49:17.315] [jointLog] [info] writing output