[2019-01-15 11:34:01.865] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 11:34:01.865] [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 11:34:01.865] [jointLog] [info] parsing read library format
[2019-01-15 11:34:01.866] [jointLog] [info] There is 1 library.
[2019-01-15 11:34:01.904] [jointLog] [info] Loading Quasi index
[2019-01-15 11:34:01.905] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 11:34:13.435] [jointLog] [info] done
[2019-01-15 11:34:13.435] [jointLog] [info] Index contained 137,271 targets
[2019-01-15 11:34:15.836] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 11:39:13.659] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2019-01-15 11:39:13.660] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2019-01-15 11:39:13.667] [jointLog] [info] Thread saw mini-batch with a maximum of 3.02% zero probability fragments
[2019-01-15 11:39:13.687] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2019-01-15 11:39:13.689] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2019-01-15 11:39:13.700] [jointLog] [info] Thread saw mini-batch with a maximum of 3.20% zero probability fragments
[2019-01-15 11:39:14.159] [jointLog] [info] Computed 266,135 rich equivalence classes for further processing
[2019-01-15 11:39:14.159] [jointLog] [info] Counted 28,326,305 total reads in the equivalence classes 
[2019-01-15 11:39:14.174] [jointLog] [info] Mapping rate = 60.4798%

[2019-01-15 11:39:14.174] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 11:39:14.181] [jointLog] [info] Starting optimizer
[2019-01-15 11:39:14.160] [fileLog] [info] 
At end of round 0
==================
Observed 46835948 total fragments (46835948 in most recent round)

[2019-01-15 11:39:27.946] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 11:39:27.962] [jointLog] [info] iteration = 0 | max rel diff. = 4150.69
[2019-01-15 11:39:28.127] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 11:41:07.574] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 11:41:07.574] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 11:41:18.891] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 11:41:31.351] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 11:41:42.431] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 11:41:53.727] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 11:42:05.031] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 11:42:16.018] [jointLog] [info] processed bias for 60.0% of the transcripts
[2019-01-15 11:42:23.063] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 11:42:24.749] [jointLog] [info] iteration = 100 | max rel diff. = 3.8594
[2019-01-15 11:42:26.483] [jointLog] [info] iteration = 200 | max rel diff. = 8.48292
[2019-01-15 11:42:28.205] [jointLog] [info] iteration = 300 | max rel diff. = 0.513587
[2019-01-15 11:42:30.079] [jointLog] [info] iteration = 400 | max rel diff. = 4.45766
[2019-01-15 11:42:31.869] [jointLog] [info] iteration = 500 | max rel diff. = 0.455252
[2019-01-15 11:42:33.574] [jointLog] [info] iteration = 600 | max rel diff. = 0.2422
[2019-01-15 11:42:35.290] [jointLog] [info] iteration = 700 | max rel diff. = 0.104702
[2019-01-15 11:42:37.066] [jointLog] [info] iteration = 800 | max rel diff. = 0.0492417
[2019-01-15 11:42:38.833] [jointLog] [info] iteration = 900 | max rel diff. = 0.209913
[2019-01-15 11:42:40.623] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.159608
[2019-01-15 11:42:42.376] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.793896
[2019-01-15 11:42:44.240] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0292613
[2019-01-15 11:42:46.226] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.136757
[2019-01-15 11:42:48.041] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0238129
[2019-01-15 11:42:49.959] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0233049
[2019-01-15 11:42:51.830] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0802178
[2019-01-15 11:42:52.100] [jointLog] [info] iteration = 1,616 | max rel diff. = 0.00280475
[2019-01-15 11:42:52.115] [jointLog] [info] Finished optimizer
[2019-01-15 11:42:52.115] [jointLog] [info] writing output 

[2019-01-15 11:42:52.749] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 11:43:17.931] [jointLog] [info] Finished Gibbs Sampler
