[2020-04-26 09:34:04.899] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 09:34:04.899] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 09:34:04.899] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 09:34:04.899] [jointLog] [info] parsing read library format
[2020-04-26 09:34:04.899] [jointLog] [info] There is 1 library.
[2020-04-26 09:34:04.953] [jointLog] [info] Loading pufferfish index
[2020-04-26 09:34:04.953] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 09:34:05.104] [jointLog] [info] done
[2020-04-26 09:34:05.104] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 09:34:05.115] [jointLog] [info] Number of decoys : 0
[2020-04-26 09:34:11.505] [fileLog] [info] 
At end of round 0
==================
Observed 2338381 total fragments (2338381 in most recent round)

[2020-04-26 09:34:11.505] [jointLog] [info] Computed 76,580 rich equivalence classes for further processing
[2020-04-26 09:34:11.505] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes 
[2020-04-26 09:34:11.522] [jointLog] [info] Number of mappings discarded because of alignment score : 536,819
[2020-04-26 09:34:11.522] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061
[2020-04-26 09:34:11.522] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 09:34:11.522] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328
[2020-04-26 09:34:11.525] [jointLog] [warning] Only 2319185 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 09:34:11.525] [jointLog] [info] Mapping rate = 99.1791%

[2020-04-26 09:34:11.525] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 09:34:11.526] [jointLog] [info] Starting optimizer
[2020-04-26 09:34:11.548] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 09:34:11.553] [jointLog] [info] iteration = 0 | max rel diff. = 4818.25
[2020-04-26 09:34:11.827] [jointLog] [info] iteration = 100 | max rel diff. = 4.54139
[2020-04-26 09:34:12.107] [jointLog] [info] iteration = 200 | max rel diff. = 0.978654
[2020-04-26 09:34:12.384] [jointLog] [info] iteration = 300 | max rel diff. = 0.940331
[2020-04-26 09:34:12.663] [jointLog] [info] iteration = 400 | max rel diff. = 0.456069
[2020-04-26 09:34:12.948] [jointLog] [info] iteration = 500 | max rel diff. = 0.973272
[2020-04-26 09:34:13.233] [jointLog] [info] iteration = 600 | max rel diff. = 0.348657
[2020-04-26 09:34:13.516] [jointLog] [info] iteration = 700 | max rel diff. = 0.0549103
[2020-04-26 09:34:13.799] [jointLog] [info] iteration = 800 | max rel diff. = 0.0267887
[2020-04-26 09:34:14.082] [jointLog] [info] iteration = 900 | max rel diff. = 0.0537841
[2020-04-26 09:34:14.365] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.33829
[2020-04-26 09:34:14.537] [jointLog] [info] iteration = 1,063 | max rel diff. = 0.00207819
[2020-04-26 09:34:14.538] [jointLog] [info] Finished optimizer
[2020-04-26 09:34:14.538] [jointLog] [info] writing output