[2020-04-30 07:05:12.730] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:05:12.730] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:05:12.730] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:05:12.730] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:05:12.730] [jointLog] [info] parsing read library format
[2020-04-30 07:05:12.730] [jointLog] [info] There is 1 library.
[2020-04-30 07:05:12.782] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:05:12.783] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information.
[2020-04-30 07:05:12.783] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:05:12.897] [jointLog] [info] done
[2020-04-30 07:05:12.897] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:05:12.913] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:05:13.937] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:05:14.265] [jointLog] [info] Computed 3,109 rich equivalence classes for further processing
[2020-04-30 07:05:14.265] [jointLog] [info] Counted 91,922 total reads in the equivalence classes 
[2020-04-30 07:05:14.295] [jointLog] [info] Number of mappings discarded because of alignment score : 81,954
[2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,702
[2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 161
[2020-04-30 07:05:14.298] [jointLog] [warning] Only 91922 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2020-04-30 07:05:14.298] [jointLog] [info] Mapping rate = 90.3197%

[2020-04-30 07:05:14.298] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:05:14.300] [jointLog] [info] Starting optimizer
[2020-04-30 07:05:14.311] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:05:14.314] [jointLog] [info] iteration = 0 | max rel diff. = 224.624
[2020-04-30 07:05:14.379] [jointLog] [info] iteration = 100 | max rel diff. = 0.396797
[2020-04-30 07:05:14.266] [fileLog] [info] 
At end of round 0
==================
Observed 101774 total fragments (101774 in most recent round)

[2020-04-30 07:05:14.435] [jointLog] [info] iteration = 200 | max rel diff. = 0.327626
[2020-04-30 07:05:14.458] [jointLog] [info] iteration = 246 | max rel diff. = 0.0063857
[2020-04-30 07:05:14.458] [jointLog] [info] Finished optimizer
[2020-04-30 07:05:14.458] [jointLog] [info] writing output