[2020-04-30 07:04:30.518] [jointLog] [info] setting maxHashResizeThreads to 28
[2020-04-30 07:04:30.518] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-30 07:04:30.518] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-30 07:04:30.518] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-30 07:04:30.518] [jointLog] [info] parsing read library format
[2020-04-30 07:04:30.519] [jointLog] [info] There is 1 library.
[2020-04-30 07:04:30.600] [jointLog] [info] Loading pufferfish index
[2020-04-30 07:04:30.600] [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 07:04:30.600] [jointLog] [info] Loading dense pufferfish index.
[2020-04-30 07:04:30.714] [jointLog] [info] done
[2020-04-30 07:04:30.714] [jointLog] [info] Index contained 40,435 targets
[2020-04-30 07:04:30.730] [jointLog] [info] Number of decoys : 0
[2020-04-30 07:04:31.463] [jointLog] [info] Automatically detected most likely library type as IU
[2020-04-30 07:04:31.741] [jointLog] [info] Computed 4,673 rich equivalence classes for further processing
[2020-04-30 07:04:31.741] [jointLog] [info] Counted 49,677 total reads in the equivalence classes 
[2020-04-30 07:04:31.790] [jointLog] [info] Number of mappings discarded because of alignment score : 42,895
[2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,613
[2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 155
[2020-04-30 07:04:31.794] [jointLog] [warning] Only 49677 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 07:04:31.794] [jointLog] [info] Mapping rate = 87.6184%

[2020-04-30 07:04:31.794] [jointLog] [info] finished quantifyLibrary()
[2020-04-30 07:04:31.795] [jointLog] [info] Starting optimizer
[2020-04-30 07:04:31.807] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-30 07:04:31.810] [jointLog] [info] iteration = 0 | max rel diff. = 110.426
[2020-04-30 07:04:31.876] [jointLog] [info] iteration = 100 | max rel diff. = 0.126652
[2020-04-30 07:04:31.899] [jointLog] [info] iteration = 139 | max rel diff. = 0.00959537
[2020-04-30 07:04:31.900] [jointLog] [info] Finished optimizer
[2020-04-30 07:04:31.900] [jointLog] [info] writing output 

[2020-04-30 07:04:31.741] [fileLog] [info] 
At end of round 0
==================
Observed 56697 total fragments (56697 in most recent round)