[2019-01-15 21:37:56.618] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 21:37:56.618] [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 21:37:56.618] [jointLog] [info] parsing read library format
[2019-01-15 21:37:56.618] [jointLog] [info] There is 1 library.
[2019-01-15 21:37:56.659] [jointLog] [info] Loading Quasi index
[2019-01-15 21:37:56.660] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 21:38:07.789] [jointLog] [info] done
[2019-01-15 21:38:07.790] [jointLog] [info] Index contained 205,870 targets
[2019-01-15 21:38:10.390] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 21:41:35.173] [jointLog] [info] Thread saw mini-batch with a maximum of 85.16% zero probability fragments
[2019-01-15 21:41:35.209] [jointLog] [info] Thread saw mini-batch with a maximum of 86.60% zero probability fragments
[2019-01-15 21:41:35.245] [jointLog] [info] Thread saw mini-batch with a maximum of 80.68% zero probability fragments
[2019-01-15 21:41:35.276] [jointLog] [info] Thread saw mini-batch with a maximum of 76.24% zero probability fragments
[2019-01-15 21:41:35.286] [jointLog] [info] Thread saw mini-batch with a maximum of 86.44% zero probability fragments
[2019-01-15 21:41:35.322] [jointLog] [info] Thread saw mini-batch with a maximum of 67.54% zero probability fragments
[2019-01-15 21:41:35.765] [fileLog] [info] 
At end of round 0
==================
Observed 40020254 total fragments (40020254 in most recent round)

[2019-01-15 21:41:35.765] [jointLog] [info] Computed 331,637 rich equivalence classes for further processing
[2019-01-15 21:41:35.765] [jointLog] [info] Counted 34,923,684 total reads in the equivalence classes 
[2019-01-15 21:41:35.778] [jointLog] [info] Mapping rate = 87.265%

[2019-01-15 21:41:35.778] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 21:41:35.783] [jointLog] [info] Starting optimizer
[2019-01-15 21:41:35.967] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 21:41:35.996] [jointLog] [info] iteration = 0 | max rel diff. = 5637.83
[2019-01-15 21:41:36.277] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 21:43:37.578] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 21:43:37.578] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 21:43:53.514] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 21:44:07.385] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 21:44:25.019] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 21:44:39.206] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 21:44:53.817] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 21:44:56.692] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 21:44:58.618] [jointLog] [info] iteration = 100 | max rel diff. = 19.7686
[2019-01-15 21:45:00.756] [jointLog] [info] iteration = 200 | max rel diff. = 6.81479
[2019-01-15 21:45:03.045] [jointLog] [info] iteration = 300 | max rel diff. = 1.91727
[2019-01-15 21:45:05.168] [jointLog] [info] iteration = 400 | max rel diff. = 0.684568
[2019-01-15 21:45:07.412] [jointLog] [info] iteration = 500 | max rel diff. = 3.66701
[2019-01-15 21:45:09.535] [jointLog] [info] iteration = 600 | max rel diff. = 2.35809
[2019-01-15 21:45:11.657] [jointLog] [info] iteration = 700 | max rel diff. = 0.1883
[2019-01-15 21:45:13.780] [jointLog] [info] iteration = 800 | max rel diff. = 0.244479
[2019-01-15 21:45:15.906] [jointLog] [info] iteration = 900 | max rel diff. = 0.13878
[2019-01-15 21:45:18.027] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.4405
[2019-01-15 21:45:20.150] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0861223
[2019-01-15 21:45:22.303] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0332279
[2019-01-15 21:45:24.799] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0512707
[2019-01-15 21:45:27.155] [jointLog] [info] iteration = 1,395 | max rel diff. = 0.00647564
[2019-01-15 21:45:27.164] [jointLog] [info] Finished optimizer
[2019-01-15 21:45:27.164] [jointLog] [info] writing output 

[2019-01-15 21:45:27.912] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 21:46:10.703] [jointLog] [info] Finished Gibbs Sampler
