[2020-04-26 07:04:30.047] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 07:04:30.047] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 07:04:30.047] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 07:04:30.047] [jointLog] [info] parsing read library format
[2020-04-26 07:04:30.047] [jointLog] [info] There is 1 library.
[2020-04-26 07:04:30.102] [jointLog] [info] Loading pufferfish index
[2020-04-26 07:04:30.103] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 07:04:30.229] [jointLog] [info] done
[2020-04-26 07:04:30.229] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 07:04:30.240] [jointLog] [info] Number of decoys : 0
[2020-04-26 07:04:36.130] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-26 07:04:36.130] [jointLog] [info] Computed 81,779 rich equivalence classes for further processing
[2020-04-26 07:04:36.130] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes 
[2020-04-26 07:04:36.151] [jointLog] [info] Number of mappings discarded because of alignment score : 733,446
[2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154
[2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582
[2020-04-26 07:04:36.154] [jointLog] [warning] Only 1745454 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 07:04:36.154] [jointLog] [info] Mapping rate = 98.6937%

[2020-04-26 07:04:36.154] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 07:04:36.156] [jointLog] [info] Starting optimizer
[2020-04-26 07:04:36.183] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 07:04:36.189] [jointLog] [info] iteration = 0 | max rel diff. = 3747.29
[2020-04-26 07:04:36.519] [jointLog] [info] iteration = 100 | max rel diff. = 4.26197
[2020-04-26 07:04:36.857] [jointLog] [info] iteration = 200 | max rel diff. = 2.41322
[2020-04-26 07:04:37.197] [jointLog] [info] iteration = 300 | max rel diff. = 1.03586
[2020-04-26 07:04:37.545] [jointLog] [info] iteration = 400 | max rel diff. = 0.0529547
[2020-04-26 07:04:37.893] [jointLog] [info] iteration = 500 | max rel diff. = 0.0102767
[2020-04-26 07:04:38.247] [jointLog] [info] iteration = 600 | max rel diff. = 0.290856
[2020-04-26 07:04:38.265] [jointLog] [info] iteration = 606 | max rel diff. = 0.00617136
[2020-04-26 07:04:38.266] [jointLog] [info] Finished optimizer
[2020-04-26 07:04:38.266] [jointLog] [info] writing output