[2020-04-26 03:57:37.504] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 03:57:37.504] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 03:57:37.504] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 03:57:37.504] [jointLog] [info] parsing read library format
[2020-04-26 03:57:37.504] [jointLog] [info] There is 1 library.
[2020-04-26 03:57:37.565] [jointLog] [info] Loading pufferfish index
[2020-04-26 03:57:37.565] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 03:57:37.648] [jointLog] [info] done
[2020-04-26 03:57:37.648] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 03:57:37.661] [jointLog] [info] Number of decoys : 0
[2020-04-26 03:57:41.608] [fileLog] [info] 
At end of round 0
==================
Observed 1320346 total fragments (1320346 in most recent round)

[2020-04-26 03:57:41.607] [jointLog] [info] Computed 70,026 rich equivalence classes for further processing
[2020-04-26 03:57:41.607] [jointLog] [info] Counted 1,295,947 total reads in the equivalence classes 
[2020-04-26 03:57:41.624] [jointLog] [info] Number of mappings discarded because of alignment score : 406,709
[2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,984
[2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002
[2020-04-26 03:57:41.628] [jointLog] [warning] Only 1295947 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 03:57:41.628] [jointLog] [info] Mapping rate = 98.1521%

[2020-04-26 03:57:41.628] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 03:57:41.629] [jointLog] [info] Starting optimizer
[2020-04-26 03:57:41.651] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 03:57:41.655] [jointLog] [info] iteration = 0 | max rel diff. = 3060.57
[2020-04-26 03:57:41.889] [jointLog] [info] iteration = 100 | max rel diff. = 7.40287
[2020-04-26 03:57:42.122] [jointLog] [info] iteration = 200 | max rel diff. = 0.190008
[2020-04-26 03:57:42.355] [jointLog] [info] iteration = 300 | max rel diff. = 0.241952
[2020-04-26 03:57:42.588] [jointLog] [info] iteration = 400 | max rel diff. = 2.06599
[2020-04-26 03:57:42.806] [jointLog] [info] iteration = 500 | max rel diff. = 15.6906
[2020-04-26 03:57:42.824] [jointLog] [info] iteration = 509 | max rel diff. = 0.00650112
[2020-04-26 03:57:42.825] [jointLog] [info] Finished optimizer
[2020-04-26 03:57:42.825] [jointLog] [info] writing output