[2020-04-26 06:35:31.171] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-26 06:35:31.171] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-26 06:35:31.171] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-26 06:35:31.171] [jointLog] [info] parsing read library format
[2020-04-26 06:35:31.171] [jointLog] [info] There is 1 library.
[2020-04-26 06:35:31.228] [jointLog] [info] Loading pufferfish index
[2020-04-26 06:35:31.228] [jointLog] [info] Loading dense pufferfish index.
[2020-04-26 06:35:31.363] [jointLog] [info] done
[2020-04-26 06:35:31.363] [jointLog] [info] Index contained 40,435 targets
[2020-04-26 06:35:31.377] [jointLog] [info] Number of decoys : 0
[2020-04-26 06:35:37.274] [fileLog] [info] 
At end of round 0
==================
Observed 1729420 total fragments (1729420 in most recent round)

[2020-04-26 06:35:37.273] [jointLog] [info] Computed 62,659 rich equivalence classes for further processing
[2020-04-26 06:35:37.273] [jointLog] [info] Counted 1,711,628 total reads in the equivalence classes 
[2020-04-26 06:35:37.293] [jointLog] [info] Number of mappings discarded because of alignment score : 553,510
[2020-04-26 06:35:37.293] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,872
[2020-04-26 06:35:37.293] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-26 06:35:37.293] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,511
[2020-04-26 06:35:37.297] [jointLog] [warning] Only 1711628 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 06:35:37.297] [jointLog] [info] Mapping rate = 98.9712%

[2020-04-26 06:35:37.297] [jointLog] [info] finished quantifyLibrary()
[2020-04-26 06:35:37.298] [jointLog] [info] Starting optimizer
[2020-04-26 06:35:37.329] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-26 06:35:37.334] [jointLog] [info] iteration = 0 | max rel diff. = 4012.48
[2020-04-26 06:35:37.598] [jointLog] [info] iteration = 100 | max rel diff. = 1.00965
[2020-04-26 06:35:37.857] [jointLog] [info] iteration = 200 | max rel diff. = 13.4679
[2020-04-26 06:35:38.110] [jointLog] [info] iteration = 300 | max rel diff. = 3.53842
[2020-04-26 06:35:38.370] [jointLog] [info] iteration = 400 | max rel diff. = 0.113016
[2020-04-26 06:35:38.630] [jointLog] [info] iteration = 500 | max rel diff. = 0.423192
[2020-04-26 06:35:38.640] [jointLog] [info] iteration = 505 | max rel diff. = 0.00414774
[2020-04-26 06:35:38.641] [jointLog] [info] Finished optimizer
[2020-04-26 06:35:38.641] [jointLog] [info] writing output