[2020-04-30 07:04:54.665] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:54.665] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:54.665] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:54.665] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:54.665] [jointLog] [info] parsing read library format
[2020-04-30 07:04:54.665] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:54.720] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:54.720] [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 07:04:54.720] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:54.834] [jointLog] [info] done
[2020-04-30 07:04:54.834] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:54.850] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:55.522] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:05:01.456] [jointLog] [info] Computed 20,097 rich equivalence classes for further processing
[2020-04-30 07:05:01.456] [jointLog] [info] Counted 1,713,501 total reads in the equivalence classes 
[2020-04-30 07:05:01.468] [jointLog] [info] Number of mappings discarded because of alignment score : 451,979
[2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,999
[2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,619
[2020-04-30 07:05:01.472] [jointLog] [warning] Only 1713501 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 07:05:01.472] [jointLog] [info] Mapping rate = 99.0795%

[2020-04-30 07:05:01.472] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:05:01.473] [jointLog] [info] Starting optimizer
[2020-04-30 07:05:01.490] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:05:01.491] [jointLog] [info] iteration = 0 | max rel diff. = 4022.53
[2020-04-30 07:05:01.584] [jointLog] [info] iteration = 100 | max rel diff. = 1.10041
[2020-04-30 07:05:01.667] [jointLog] [info] iteration = 200 | max rel diff. = 2.06161
[2020-04-30 07:05:01.747] [jointLog] [info] iteration = 300 | max rel diff. = 1.18506
[2020-04-30 07:05:01.827] [jointLog] [info] iteration = 400 | max rel diff. = 0.0532494
[2020-04-30 07:05:01.457] [fileLog] [info] 
At end of round 0
==================
Observed 1729420 total fragments (1729420 in most recent round)

[2020-04-30 07:05:01.904] [jointLog] [info] iteration = 500 | max rel diff. = 0.768103
[2020-04-30 07:05:01.939] [jointLog] [info] iteration = 549 | max rel diff. = 0.00563838
[2020-04-30 07:05:01.939] [jointLog] [info] Finished optimizer
[2020-04-30 07:05:01.939] [jointLog] [info] writing output