[2020-04-30 07:02:31.546] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:02:31.546] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:02:31.546] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:02:31.546] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:02:31.546] [jointLog] [info] parsing read library format
[2020-04-30 07:02:31.546] [jointLog] [info] There is 1 library.
[2020-04-30 07:02:31.614] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:02:31.614] [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 07:02:31.614] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:02:32.344] [jointLog] [info] done
[2020-04-30 07:02:32.344] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:02:32.373] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:02:33.096] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:02:38.756] [jointLog] [info] Computed 23,977 rich equivalence classes for further processing
[2020-04-30 07:02:38.756] [jointLog] [info] Counted 1,748,058 total reads in the equivalence classes 
[2020-04-30 07:02:38.768] [jointLog] [info] Number of mappings discarded because of alignment score : 527,438
[2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,550
[2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,439
[2020-04-30 07:02:38.771] [jointLog] [warning] Only 1748058 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 07:02:38.771] [jointLog] [info] Mapping rate = 98.841%

[2020-04-30 07:02:38.771] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:02:38.772] [jointLog] [info] Starting optimizer
[2020-04-30 07:02:38.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:02:38.792] [jointLog] [info] iteration = 0 | max rel diff. = 3792.63
[2020-04-30 07:02:38.907] [jointLog] [info] iteration = 100 | max rel diff. = 18.3887
[2020-04-30 07:02:38.986] [jointLog] [info] iteration = 200 | max rel diff. = 0.501756
[2020-04-30 07:02:39.064] [jointLog] [info] iteration = 300 | max rel diff. = 1.48997
[2020-04-30 07:02:39.141] [jointLog] [info] iteration = 400 | max rel diff. = 0.22212
[2020-04-30 07:02:39.219] [jointLog] [info] iteration = 500 | max rel diff. = 0.0265549
[2020-04-30 07:02:38.757] [fileLog] [info] 
At end of round 0
==================
Observed 1768556 total fragments (1768556 in most recent round)

[2020-04-30 07:02:39.296] [jointLog] [info] iteration = 600 | max rel diff. = 0.101989
[2020-04-30 07:02:39.304] [jointLog] [info] iteration = 612 | max rel diff. = 0.00444295
[2020-04-30 07:02:39.305] [jointLog] [info] Finished optimizer
[2020-04-30 07:02:39.305] [jointLog] [info] writing output