[2020-04-26 08:13:43.013] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 08:13:43.013] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 08:13:43.013] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 08:13:43.013] [jointLog] [info] parsing read library format
[2020-04-26 08:13:43.013] [jointLog] [info] There is 1 library.
[2020-04-26 08:13:43.082] [jointLog] [info] Loading pufferfish index
[2020-04-26 08:13:43.082] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 08:13:43.201] [jointLog] [info] done
[2020-04-26 08:13:43.201] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 08:13:43.214] [jointLog] [info] Number of decoys : 0
[2020-04-26 08:13:52.372] [jointLog] [info] Computed 95,533 rich equivalence classes for further processing
[2020-04-26 08:13:52.372] [jointLog] [info] Counted 3,196,425 total reads in the equivalence classes 
[2020-04-26 08:13:52.392] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,611
[2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,486
[2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462
[2020-04-26 08:13:52.396] [jointLog] [warning] Only 3196425 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 08:13:52.396] [jointLog] [info] Mapping rate = 99.2016%

[2020-04-26 08:13:52.396] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 08:13:52.398] [jointLog] [info] Starting optimizer
[2020-04-26 08:13:52.424] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 08:13:52.433] [jointLog] [info] iteration = 0 | max rel diff. = 7373.04
[2020-04-26 08:13:52.372] [fileLog] [info] 
At end of round 0
==================
Observed 3222151 total fragments (3222151 in most recent round)

[2020-04-26 08:13:52.812] [jointLog] [info] iteration = 100 | max rel diff. = 14.7581
[2020-04-26 08:13:53.191] [jointLog] [info] iteration = 200 | max rel diff. = 7.33361
[2020-04-26 08:13:53.573] [jointLog] [info] iteration = 300 | max rel diff. = 1.83114
[2020-04-26 08:13:53.954] [jointLog] [info] iteration = 400 | max rel diff. = 0.279964
[2020-04-26 08:13:54.336] [jointLog] [info] iteration = 500 | max rel diff. = 0.151216
[2020-04-26 08:13:54.722] [jointLog] [info] iteration = 600 | max rel diff. = 0.0835096
[2020-04-26 08:13:55.105] [jointLog] [info] iteration = 700 | max rel diff. = 0.0311626
[2020-04-26 08:13:55.484] [jointLog] [info] iteration = 800 | max rel diff. = 0.030291
[2020-04-26 08:13:55.607] [jointLog] [info] iteration = 833 | max rel diff. = 0.00668361
[2020-04-26 08:13:55.611] [jointLog] [info] Finished optimizer
[2020-04-26 08:13:55.611] [jointLog] [info] writing output