[2020-04-26 01:53:36.352] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 01:53:36.352] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 01:53:36.352] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 01:53:36.352] [jointLog] [info] parsing read library format
[2020-04-26 01:53:36.352] [jointLog] [info] There is 1 library.
[2020-04-26 01:53:36.404] [jointLog] [info] Loading pufferfish index
[2020-04-26 01:53:36.404] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 01:53:36.480] [jointLog] [info] done
[2020-04-26 01:53:36.480] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 01:53:36.492] [jointLog] [info] Number of decoys : 0
[2020-04-26 01:53:45.862] [fileLog] [info] 
At end of round 0
==================
Observed 3222151 total fragments (3222151 in most recent round)

[2020-04-26 01:53:45.861] [jointLog] [info] Computed 95,566 rich equivalence classes for further processing
[2020-04-26 01:53:45.861] [jointLog] [info] Counted 3,196,427 total reads in the equivalence classes 
[2020-04-26 01:53:45.881] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,607
[2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,484
[2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462
[2020-04-26 01:53:45.884] [jointLog] [warning] Only 3196427 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 01:53:45.884] [jointLog] [info] Mapping rate = 99.2017%

[2020-04-26 01:53:45.884] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 01:53:45.885] [jointLog] [info] Starting optimizer
[2020-04-26 01:53:45.910] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 01:53:45.917] [jointLog] [info] iteration = 0 | max rel diff. = 7372.2
[2020-04-26 01:53:46.322] [jointLog] [info] iteration = 100 | max rel diff. = 16.4913
[2020-04-26 01:53:46.723] [jointLog] [info] iteration = 200 | max rel diff. = 11.3941
[2020-04-26 01:53:47.118] [jointLog] [info] iteration = 300 | max rel diff. = 0.735245
[2020-04-26 01:53:47.515] [jointLog] [info] iteration = 400 | max rel diff. = 0.351225
[2020-04-26 01:53:47.908] [jointLog] [info] iteration = 500 | max rel diff. = 0.154959
[2020-04-26 01:53:48.309] [jointLog] [info] iteration = 600 | max rel diff. = 0.0119094
[2020-04-26 01:53:48.702] [jointLog] [info] iteration = 700 | max rel diff. = 0.0420495
[2020-04-26 01:53:49.093] [jointLog] [info] iteration = 800 | max rel diff. = 0.0424652
[2020-04-26 01:53:49.257] [jointLog] [info] iteration = 843 | max rel diff. = 0.00706082
[2020-04-26 01:53:49.259] [jointLog] [info] Finished optimizer
[2020-04-26 01:53:49.259] [jointLog] [info] writing output