[2020-04-30 07:04:03.955] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:03.955] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:03.955] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:03.955] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:03.955] [jointLog] [info] parsing read library format
[2020-04-30 07:04:03.955] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:04.040] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:04.041] [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 07:04:04.041] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:04.159] [jointLog] [info] done
[2020-04-30 07:04:04.159] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:04.175] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:05.019] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:09.346] [jointLog] [info] Computed 15,856 rich equivalence classes for further processing
[2020-04-30 07:04:09.346] [jointLog] [info] Counted 1,108,997 total reads in the equivalence classes 
[2020-04-30 07:04:09.358] [jointLog] [info] Number of mappings discarded because of alignment score : 362,640
[2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 10,615
[2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,854
[2020-04-30 07:04:09.362] [jointLog] [warning] Only 1108997 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 07:04:09.362] [jointLog] [info] Mapping rate = 99.0177%

[2020-04-30 07:04:09.362] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:09.363] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:09.378] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:09.380] [jointLog] [info] iteration = 0 | max rel diff. = 2470.87
[2020-04-30 07:04:09.487] [jointLog] [info] iteration = 100 | max rel diff. = 0.279124
[2020-04-30 07:04:09.567] [jointLog] [info] iteration = 200 | max rel diff. = 0.824234
[2020-04-30 07:04:09.347] [fileLog] [info] 
At end of round 0
==================
Observed 1119999 total fragments (1119999 in most recent round)

[2020-04-30 07:04:09.642] [jointLog] [info] iteration = 300 | max rel diff. = 0.488518
[2020-04-30 07:04:09.717] [jointLog] [info] iteration = 400 | max rel diff. = 0.0322291
[2020-04-30 07:04:09.753] [jointLog] [info] iteration = 449 | max rel diff. = 0.00615236
[2020-04-30 07:04:09.754] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:09.754] [jointLog] [info] writing output