[2020-04-30 07:04:48.299] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:48.299] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:48.299] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:48.299] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:48.299] [jointLog] [info] parsing read library format
[2020-04-30 07:04:48.299] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:48.349] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:48.349] [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 07:04:48.349] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:48.456] [jointLog] [info] done
[2020-04-30 07:04:48.456] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:48.472] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:49.059] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:52.325] [jointLog] [info] Computed 32,026 rich equivalence classes for further processing
[2020-04-30 07:04:52.325] [jointLog] [info] Counted 1,297,181 total reads in the equivalence classes 
[2020-04-30 07:04:52.337] [jointLog] [info] Number of mappings discarded because of alignment score : 334,174
[2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,750
[2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,625
[2020-04-30 07:04:52.340] [jointLog] [warning] Only 1297181 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 07:04:52.340] [jointLog] [info] Mapping rate = 98.2455%

[2020-04-30 07:04:52.340] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:52.341] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:52.354] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:52.356] [jointLog] [info] iteration = 0 | max rel diff. = 3070.88
[2020-04-30 07:04:52.462] [jointLog] [info] iteration = 100 | max rel diff. = 5.86972
[2020-04-30 07:04:52.325] [fileLog] [info] 
At end of round 0
==================
Observed 1320346 total fragments (1320346 in most recent round)

[2020-04-30 07:04:52.552] [jointLog] [info] iteration = 200 | max rel diff. = 1.88549
[2020-04-30 07:04:52.638] [jointLog] [info] iteration = 300 | max rel diff. = 0.276806
[2020-04-30 07:04:52.724] [jointLog] [info] iteration = 400 | max rel diff. = 0.736597
[2020-04-30 07:04:52.810] [jointLog] [info] iteration = 500 | max rel diff. = 12.4966
[2020-04-30 07:04:52.815] [jointLog] [info] iteration = 506 | max rel diff. = 0.0075709
[2020-04-30 07:04:52.815] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:52.815] [jointLog] [info] writing output