[2020-04-30 07:02:40.893] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:40.893] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:40.893] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:40.893] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:40.893] [jointLog] [info] parsing read library format
[2020-04-30 07:02:40.893] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:40.945] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:40.945] [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 07:02:40.945] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:41.059] [jointLog] [info] done
[2020-04-30 07:02:41.059] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:41.075] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:41.932] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:02:53.428] [jointLog] [info] Computed 34,832 rich equivalence classes for further processing
[2020-04-30 07:02:53.428] [jointLog] [info] Counted 4,281,878 total reads in the equivalence classes 
[2020-04-30 07:02:53.440] [jointLog] [info] Number of mappings discarded because of alignment score : 900,934
[2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 27,361
[2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,757
[2020-04-30 07:02:53.443] [jointLog] [warning] Only 4281878 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 07:02:53.443] [jointLog] [info] Mapping rate = 99.3236%

[2020-04-30 07:02:53.443] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:02:53.444] [jointLog] [info] Starting optimizer
[2020-04-30 07:02:53.460] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:02:53.461] [jointLog] [info] iteration = 0 | max rel diff. = 9627.48
[2020-04-30 07:02:53.567] [jointLog] [info] iteration = 100 | max rel diff. = 10.5111
[2020-04-30 07:02:53.429] [fileLog] [info] 
At end of round 0
==================
Observed 4311037 total fragments (4311037 in most recent round)

[2020-04-30 07:02:53.658] [jointLog] [info] iteration = 200 | max rel diff. = 11.0011
[2020-04-30 07:02:53.746] [jointLog] [info] iteration = 300 | max rel diff. = 0.306574
[2020-04-30 07:02:53.834] [jointLog] [info] iteration = 400 | max rel diff. = 3.82001
[2020-04-30 07:02:53.921] [jointLog] [info] iteration = 500 | max rel diff. = 18.5265
[2020-04-30 07:02:54.008] [jointLog] [info] iteration = 600 | max rel diff. = 0.179279
[2020-04-30 07:02:54.096] [jointLog] [info] iteration = 700 | max rel diff. = 0.0595298
[2020-04-30 07:02:54.183] [jointLog] [info] iteration = 800 | max rel diff. = 0.507489
[2020-04-30 07:02:54.243] [jointLog] [info] iteration = 871 | max rel diff. = 0.00340919
[2020-04-30 07:02:54.244] [jointLog] [info] Finished optimizer
[2020-04-30 07:02:54.244] [jointLog] [info] writing output