[2019-01-30 21:12:16.046] [jointLog] [info] parsing read library format
[2019-01-30 21:12:16.046] [jointLog] [info] There is 1 library.
[2019-01-30 21:12:16.106] [jointLog] [info] Loading Quasi index
[2019-01-30 21:12:16.106] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:12:16.496] [jointLog] [info] done
[2019-01-30 21:12:16.496] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:13:24.533] [jointLog] [info] Computed 7401 rich equivalence classes for further processing
[2019-01-30 21:13:24.533] [jointLog] [info] Counted 2716216 total reads in the equivalence classes 
[2019-01-30 21:13:24.543] [jointLog] [warning] 0.0118102% 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 21:13:24.544] [jointLog] [warning] Only 2716216 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 21:13:24.544] [jointLog] [info] Mapping rate = 9.59013%

[2019-01-30 21:13:24.544] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:13:24.544] [jointLog] [info] Starting optimizer
[2019-01-30 21:13:24.550] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:13:24.551] [jointLog] [info] iteration = 0 | max rel diff. = 623.195
[2019-01-30 21:13:24.573] [jointLog] [info] iteration = 100 | max rel diff. = 0.126869
[2019-01-30 21:13:24.591] [jointLog] [info] iteration = 200 | max rel diff. = 0.0632856
[2019-01-30 21:13:24.609] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433748
[2019-01-30 21:13:24.626] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310135
[2019-01-30 21:13:24.644] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246257
[2019-01-30 21:13:24.662] [jointLog] [info] iteration = 600 | max rel diff. = 0.0180863
[2019-01-30 21:13:24.533] [fileLog] [info] 
At end of round 0
==================
Observed 28323045 total fragments (28323045 in most recent round)

[2019-01-30 21:13:24.680] [jointLog] [info] iteration = 700 | max rel diff. = 0.015206
[2019-01-30 21:13:24.698] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135994
[2019-01-30 21:13:24.716] [jointLog] [info] iteration = 900 | max rel diff. = 0.0118754
[2019-01-30 21:13:24.735] [jointLog] [info] iteration = 1000 | max rel diff. = 0.011097
[2019-01-30 21:13:24.741] [jointLog] [info] iteration = 1035 | max rel diff. = 0.00985433
[2019-01-30 21:13:24.741] [jointLog] [info] Finished optimizer
[2019-01-30 21:13:24.741] [jointLog] [info] writing output 

[2019-01-30 21:13:24.754] [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_04/lib_format_counts.json for details