[2019-01-30 21:16:52.326] [jointLog] [info] parsing read library format
[2019-01-30 21:16:52.326] [jointLog] [info] There is 1 library.
[2019-01-30 21:16:52.388] [jointLog] [info] Loading Quasi index
[2019-01-30 21:16:52.388] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:16:52.775] [jointLog] [info] done
[2019-01-30 21:16:52.775] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:18:08.800] [jointLog] [info] Computed 8044 rich equivalence classes for further processing
[2019-01-30 21:18:08.800] [jointLog] [info] Counted 2909485 total reads in the equivalence classes 
[2019-01-30 21:18:08.812] [jointLog] [warning] 0.0123607% 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 21:18:08.813] [jointLog] [warning] Only 2909485 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 21:18:08.813] [jointLog] [info] Mapping rate = 9.19069%

[2019-01-30 21:18:08.813] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:18:08.813] [jointLog] [info] Starting optimizer
[2019-01-30 21:18:08.818] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:18:08.818] [jointLog] [info] iteration = 0 | max rel diff. = 793.502
[2019-01-30 21:18:08.835] [jointLog] [info] iteration = 100 | max rel diff. = 0.119636
[2019-01-30 21:18:08.851] [jointLog] [info] iteration = 200 | max rel diff. = 0.0542236
[2019-01-30 21:18:08.866] [jointLog] [info] iteration = 300 | max rel diff. = 0.0369931
[2019-01-30 21:18:08.882] [jointLog] [info] iteration = 400 | max rel diff. = 0.0286885
[2019-01-30 21:18:08.898] [jointLog] [info] iteration = 500 | max rel diff. = 0.023342
[2019-01-30 21:18:08.914] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174684
[2019-01-30 21:18:08.929] [jointLog] [info] iteration = 700 | max rel diff. = 0.0169584
[2019-01-30 21:18:08.945] [jointLog] [info] iteration = 800 | max rel diff. = 0.0155419
[2019-01-30 21:18:08.960] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113094
[2019-01-30 21:18:08.801] [fileLog] [info] 
At end of round 0
==================
Observed 31656864 total fragments (31656864 in most recent round)

[2019-01-30 21:18:08.976] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0104464
[2019-01-30 21:18:08.991] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102824
[2019-01-30 21:18:08.993] [jointLog] [info] iteration = 1114 | max rel diff. = 0.0088728
[2019-01-30 21:18:08.994] [jointLog] [info] Finished optimizer
[2019-01-30 21:18:08.994] [jointLog] [info] writing output 

[2019-01-30 21:18:09.005] [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_44_03/lib_format_counts.json for details