[2019-01-15 21:13:38.570] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 21:13:38.570] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-01-15 21:13:38.570] [jointLog] [info] parsing read library format
[2019-01-15 21:13:38.570] [jointLog] [info] There is 1 library.
[2019-01-15 21:13:38.625] [jointLog] [info] Loading Quasi index
[2019-01-15 21:13:38.638] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 21:13:52.110] [jointLog] [info] done
[2019-01-15 21:13:52.110] [jointLog] [info] Index contained 205,870 targets
[2019-01-15 21:13:56.411] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 21:17:43.662] [jointLog] [info] Thread saw mini-batch with a maximum of 67.96% zero probability fragments
[2019-01-15 21:17:43.749] [jointLog] [info] Thread saw mini-batch with a maximum of 67.22% zero probability fragments
[2019-01-15 21:17:43.762] [jointLog] [info] Thread saw mini-batch with a maximum of 69.14% zero probability fragments
[2019-01-15 21:17:43.790] [jointLog] [info] Thread saw mini-batch with a maximum of 55.56% zero probability fragments
[2019-01-15 21:17:43.810] [jointLog] [info] Thread saw mini-batch with a maximum of 53.26% zero probability fragments
[2019-01-15 21:17:43.821] [jointLog] [info] Thread saw mini-batch with a maximum of 67.52% zero probability fragments
[2019-01-15 21:17:44.389] [fileLog] [info] 
At end of round 0
==================
Observed 49558286 total fragments (49558286 in most recent round)

[2019-01-15 21:17:44.389] [jointLog] [info] Computed 393,846 rich equivalence classes for further processing
[2019-01-15 21:17:44.389] [jointLog] [info] Counted 45,746,950 total reads in the equivalence classes 
[2019-01-15 21:17:44.405] [jointLog] [info] Mapping rate = 92.3094%

[2019-01-15 21:17:44.405] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 21:17:44.412] [jointLog] [info] Starting optimizer
[2019-01-15 21:17:44.663] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 21:17:44.705] [jointLog] [info] iteration = 0 | max rel diff. = 2131.43
[2019-01-15 21:17:45.119] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 21:19:10.107] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 21:19:10.107] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 21:19:22.096] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 21:19:33.143] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 21:19:43.671] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 21:19:55.314] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 21:20:07.242] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 21:20:17.282] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 21:20:19.615] [jointLog] [info] iteration = 100 | max rel diff. = 6.05116
[2019-01-15 21:20:22.797] [jointLog] [info] iteration = 200 | max rel diff. = 18.4748
[2019-01-15 21:20:25.583] [jointLog] [info] iteration = 300 | max rel diff. = 1.78064
[2019-01-15 21:20:28.899] [jointLog] [info] iteration = 400 | max rel diff. = 10.6392
[2019-01-15 21:20:32.832] [jointLog] [info] iteration = 500 | max rel diff. = 1.52549
[2019-01-15 21:20:36.116] [jointLog] [info] iteration = 600 | max rel diff. = 19.3142
[2019-01-15 21:20:39.108] [jointLog] [info] iteration = 700 | max rel diff. = 0.138224
[2019-01-15 21:20:41.837] [jointLog] [info] iteration = 800 | max rel diff. = 1.29553
[2019-01-15 21:20:44.727] [jointLog] [info] iteration = 900 | max rel diff. = 0.427475
[2019-01-15 21:20:48.409] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.139124
[2019-01-15 21:20:51.908] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0988941
[2019-01-15 21:20:55.263] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0831491
[2019-01-15 21:20:58.031] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0954854
[2019-01-15 21:21:00.888] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0270362
[2019-01-15 21:21:03.266] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0230829
[2019-01-15 21:21:05.719] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0194518
[2019-01-15 21:21:08.154] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.0493705
[2019-01-15 21:21:09.910] [jointLog] [info] iteration = 1,774 | max rel diff. = 0.00985497
[2019-01-15 21:21:09.949] [jointLog] [info] Finished optimizer
[2019-01-15 21:21:09.949] [jointLog] [info] writing output 

[2019-01-15 21:21:10.620] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 21:22:15.498] [jointLog] [info] Finished Gibbs Sampler
