[2019-01-30 21:13:25.175] [jointLog] [info] parsing read library format
[2019-01-30 21:13:25.175] [jointLog] [info] There is 1 library.
[2019-01-30 21:13:25.236] [jointLog] [info] Loading Quasi index
[2019-01-30 21:13:25.236] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:13:25.641] [jointLog] [info] done
[2019-01-30 21:13:25.641] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:14:17.684] [jointLog] [info] Computed 6922 rich equivalence classes for further processing
[2019-01-30 21:14:17.684] [jointLog] [info] Counted 1916701 total reads in the equivalence classes 
[2019-01-30 21:14:17.695] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-01-30 21:14:17.695] [jointLog] [warning] Only 1916701 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:14:17.695] [jointLog] [info] Mapping rate = 8.75913%

[2019-01-30 21:14:17.695] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:14:17.695] [jointLog] [info] Starting optimizer
[2019-01-30 21:14:17.700] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:14:17.701] [jointLog] [info] iteration = 0 | max rel diff. = 428.666
[2019-01-30 21:14:17.718] [jointLog] [info] iteration = 100 | max rel diff. = 0.11263
[2019-01-30 21:14:17.734] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561102
[2019-01-30 21:14:17.749] [jointLog] [info] iteration = 300 | max rel diff. = 0.0366455
[2019-01-30 21:14:17.764] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243092
[2019-01-30 21:14:17.779] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243105
[2019-01-30 21:14:17.684] [fileLog] [info] 
At end of round 0
==================
Observed 21882333 total fragments (21882333 in most recent round)

[2019-01-30 21:14:17.794] [jointLog] [info] iteration = 600 | max rel diff. = 0.017536
[2019-01-30 21:14:17.812] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150939
[2019-01-30 21:14:17.830] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129985
[2019-01-30 21:14:17.848] [jointLog] [info] iteration = 900 | max rel diff. = 0.011836
[2019-01-30 21:14:17.865] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0118362
[2019-01-30 21:14:17.874] [jointLog] [info] iteration = 1050 | max rel diff. = 0.00947587
[2019-01-30 21:14:17.875] [jointLog] [info] Finished optimizer
[2019-01-30 21:14:17.875] [jointLog] [info] writing output 

[2019-01-30 21:14:17.885] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_05/lib_format_counts.json for details