[2020-04-30 07:02:56.193] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:56.193] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:56.193] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:56.193] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:56.193] [jointLog] [info] parsing read library format
[2020-04-30 07:02:56.193] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:56.281] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:56.281] [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 07:02:56.281] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:56.393] [jointLog] [info] done
[2020-04-30 07:02:56.393] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:56.410] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:57.084] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:03:01.464] [jointLog] [info] Computed 13,995 rich equivalence classes for further processing
[2020-04-30 07:03:01.464] [jointLog] [info] Counted 1,455,183 total reads in the equivalence classes 
[2020-04-30 07:03:01.476] [jointLog] [info] Number of mappings discarded because of alignment score : 418,254
[2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,284
[2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,337
[2020-04-30 07:03:01.479] [jointLog] [warning] Only 1455183 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 07:03:01.479] [jointLog] [info] Mapping rate = 98.7505%

[2020-04-30 07:03:01.479] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:03:01.480] [jointLog] [info] Starting optimizer
[2020-04-30 07:03:01.492] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:03:01.495] [jointLog] [info] iteration = 0 | max rel diff. = 3460.05
[2020-04-30 07:03:01.589] [jointLog] [info] iteration = 100 | max rel diff. = 3.73156
[2020-04-30 07:03:01.657] [jointLog] [info] iteration = 200 | max rel diff. = 0.676305
[2020-04-30 07:03:01.718] [jointLog] [info] iteration = 300 | max rel diff. = 0.0691932
[2020-04-30 07:03:01.779] [jointLog] [info] iteration = 400 | max rel diff. = 0.0638414
[2020-04-30 07:03:01.831] [jointLog] [info] iteration = 487 | max rel diff. = 0.00441576
[2020-04-30 07:03:01.832] [jointLog] [info] Finished optimizer
[2020-04-30 07:03:01.832] [jointLog] [info] writing output 

[2020-04-30 07:03:01.465] [fileLog] [info] 
At end of round 0
==================
Observed 1473595 total fragments (1473595 in most recent round)