[2021-03-28 02:35:20.527] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-28 02:35:20.527] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-28 02:35:20.527] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-28 02:35:20.527] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-28 02:35:20.527] [jointLog] [info] parsing read library format
[2021-03-28 02:35:20.527] [jointLog] [info] There is 1 library.
[2021-03-28 02:35:20.668] [jointLog] [info] Loading pufferfish index
[2021-03-28 02:35:20.668] [jointLog] [info] Loading dense pufferfish index.
[2021-03-28 02:37:09.374] [jointLog] [info] done
[2021-03-28 02:37:09.374] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-28 02:38:04.640] [jointLog] [info] Number of decoys : 194
[2021-03-28 02:38:04.640] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-28 02:38:06.415] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-28 02:38:06.814] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-28 02:40:12.136] [fileLog] [info] 
At end of round 0
==================
Observed 19529164 total fragments (19529164 in most recent round)

[2021-03-28 02:40:12.135] [jointLog] [info] Computed 449,096 rich equivalence classes for further processing
[2021-03-28 02:40:12.135] [jointLog] [info] Counted 18,925,055 total reads in the equivalence classes 
[2021-03-28 02:40:12.151] [jointLog] [info] Number of mappings discarded because of alignment score : 9,687,052
[2021-03-28 02:40:12.151] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 320,607
[2021-03-28 02:40:12.151] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 276,666
[2021-03-28 02:40:12.151] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-28 02:40:12.151] [jointLog] [info] Mapping rate = 96.9066%

[2021-03-28 02:40:12.151] [jointLog] [info] finished quantifyLibrary()
[2021-03-28 02:40:12.151] [jointLog] [info] Starting optimizer
[2021-03-28 02:40:16.442] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-28 02:40:16.790] [jointLog] [info] iteration = 0 | max rel diff. = 555.288
[2021-03-28 02:40:20.285] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-28 02:42:26.458] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-28 02:42:26.458] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-28 02:42:37.926] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-28 02:42:49.726] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-28 02:43:01.586] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-28 02:43:13.484] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-28 02:43:25.229] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-28 02:43:37.357] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-28 02:43:48.721] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-28 02:44:00.339] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-28 02:44:11.906] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-28 02:44:23.205] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-28 02:44:23.208] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-28 02:44:55.414] [jointLog] [info] iteration = 100 | max rel diff. = 6.00687
[2021-03-28 02:45:30.717] [jointLog] [info] iteration = 200 | max rel diff. = 17.9054
[2021-03-28 02:46:05.862] [jointLog] [info] iteration = 300 | max rel diff. = 18.3926
[2021-03-28 02:46:40.557] [jointLog] [info] iteration = 400 | max rel diff. = 0.56333
[2021-03-28 02:47:15.141] [jointLog] [info] iteration = 500 | max rel diff. = 1.61837
[2021-03-28 02:47:49.685] [jointLog] [info] iteration = 600 | max rel diff. = 0.167403
[2021-03-28 02:48:24.018] [jointLog] [info] iteration = 700 | max rel diff. = 0.0952347
[2021-03-28 02:48:58.308] [jointLog] [info] iteration = 800 | max rel diff. = 0.112435
[2021-03-28 02:49:32.717] [jointLog] [info] iteration = 900 | max rel diff. = 0.193125
[2021-03-28 02:50:06.860] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.689186
[2021-03-28 02:50:11.684] [jointLog] [info] iteration = 1,015 | max rel diff. = 0.00931219
[2021-03-28 02:50:13.522] [jointLog] [info] Finished optimizer
[2021-03-28 02:50:13.522] [jointLog] [info] writing output