[2019-01-15 21:30:30.679] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-01-15 21:30:30.679] [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 21:30:30.679] [jointLog] [info] parsing read library format
[2019-01-15 21:30:30.679] [jointLog] [info] There is 1 library.
[2019-01-15 21:30:30.720] [jointLog] [info] Loading Quasi index
[2019-01-15 21:30:30.720] [jointLog] [info] Loading 32-bit quasi index
[2019-01-15 21:30:42.298] [jointLog] [info] done
[2019-01-15 21:30:42.298] [jointLog] [info] Index contained 205,870 targets
[2019-01-15 21:30:45.081] [jointLog] [info] Automatically detected most likely library type as ISR
[2019-01-15 21:33:35.240] [jointLog] [info] Thread saw mini-batch with a maximum of 77.32% zero probability fragments
[2019-01-15 21:33:35.273] [jointLog] [info] Thread saw mini-batch with a maximum of 75.32% zero probability fragments
[2019-01-15 21:33:35.279] [jointLog] [info] Thread saw mini-batch with a maximum of 50.16% zero probability fragments
[2019-01-15 21:33:35.297] [jointLog] [info] Thread saw mini-batch with a maximum of 75.72% zero probability fragments
[2019-01-15 21:33:35.297] [jointLog] [info] Thread saw mini-batch with a maximum of 79.50% zero probability fragments
[2019-01-15 21:33:35.321] [jointLog] [info] Thread saw mini-batch with a maximum of 78.58% zero probability fragments
[2019-01-15 21:33:35.759] [jointLog] [info] Computed 338,084 rich equivalence classes for further processing
[2019-01-15 21:33:35.759] [jointLog] [info] Counted 39,702,126 total reads in the equivalence classes 
[2019-01-15 21:33:35.771] [jointLog] [info] Mapping rate = 91.349%

[2019-01-15 21:33:35.771] [jointLog] [info] finished quantifyLibrary()
[2019-01-15 21:33:35.777] [jointLog] [info] Starting optimizer
[2019-01-15 21:33:35.949] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-15 21:33:35.759] [fileLog] [info] 
At end of round 0
==================
Observed 43462017 total fragments (43462017 in most recent round)

[2019-01-15 21:33:35.978] [jointLog] [info] iteration = 0 | max rel diff. = 4713.08
[2019-01-15 21:33:36.255] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2019-01-15 21:35:14.824] [jointLog] [info] Computed expected counts (for bias correction)
[2019-01-15 21:35:14.824] [jointLog] [info] processed bias for 0.0% of the transcripts
[2019-01-15 21:35:28.133] [jointLog] [info] processed bias for 10.0% of the transcripts
[2019-01-15 21:35:40.715] [jointLog] [info] processed bias for 20.0% of the transcripts
[2019-01-15 21:35:54.254] [jointLog] [info] processed bias for 30.0% of the transcripts
[2019-01-15 21:36:07.051] [jointLog] [info] processed bias for 40.0% of the transcripts
[2019-01-15 21:36:20.534] [jointLog] [info] processed bias for 50.0% of the transcripts
[2019-01-15 21:36:23.513] [jointLog] [info] processed bias for 100.0% of the transcripts
[2019-01-15 21:36:25.454] [jointLog] [info] iteration = 100 | max rel diff. = 12.8901
[2019-01-15 21:36:27.717] [jointLog] [info] iteration = 200 | max rel diff. = 19.2035
[2019-01-15 21:36:30.317] [jointLog] [info] iteration = 300 | max rel diff. = 2.78551
[2019-01-15 21:36:32.930] [jointLog] [info] iteration = 400 | max rel diff. = 20.2639
[2019-01-15 21:36:35.201] [jointLog] [info] iteration = 500 | max rel diff. = 8.79977
[2019-01-15 21:36:37.389] [jointLog] [info] iteration = 600 | max rel diff. = 0.279507
[2019-01-15 21:36:39.535] [jointLog] [info] iteration = 700 | max rel diff. = 5.36212
[2019-01-15 21:36:41.672] [jointLog] [info] iteration = 800 | max rel diff. = 0.315675
[2019-01-15 21:36:44.158] [jointLog] [info] iteration = 900 | max rel diff. = 0.621242
[2019-01-15 21:36:46.711] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.11923
[2019-01-15 21:36:49.098] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0691589
[2019-01-15 21:36:51.390] [jointLog] [info] iteration = 1,200 | max rel diff. = 12.1308
[2019-01-15 21:36:53.701] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0594875
[2019-01-15 21:36:55.999] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0428581
[2019-01-15 21:36:56.732] [jointLog] [info] iteration = 1,433 | max rel diff. = 0.00868595
[2019-01-15 21:36:56.741] [jointLog] [info] Finished optimizer
[2019-01-15 21:36:56.741] [jointLog] [info] writing output 

[2019-01-15 21:36:57.411] [jointLog] [info] Starting Gibbs Sampler
[2019-01-15 21:37:48.722] [jointLog] [info] Finished Gibbs Sampler
