[2021-03-23 16:37:16.506] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-23 16:37:16.506] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-23 16:37:16.506] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-23 16:37:16.506] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-23 16:37:16.506] [jointLog] [info] parsing read library format
[2021-03-23 16:37:16.506] [jointLog] [info] There is 1 library.
[2021-03-23 16:37:16.572] [jointLog] [info] Loading pufferfish index
[2021-03-23 16:37:16.572] [jointLog] [info] Loading dense pufferfish index.
[2021-03-23 16:39:00.613] [jointLog] [info] done
[2021-03-23 16:39:00.613] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-23 16:39:50.662] [jointLog] [info] Number of decoys : 194
[2021-03-23 16:39:50.662] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-23 16:39:51.684] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-23 16:39:52.430] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-23 16:41:56.478] [jointLog] [info] Computed 403,525 rich equivalence classes for further processing
[2021-03-23 16:41:56.478] [jointLog] [info] Counted 13,948,851 total reads in the equivalence classes 
[2021-03-23 16:41:56.490] [jointLog] [info] Number of mappings discarded because of alignment score : 16,281,499
[2021-03-23 16:41:56.490] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 375,756
[2021-03-23 16:41:56.490] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 219,819
[2021-03-23 16:41:56.490] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-23 16:41:56.490] [jointLog] [info] Mapping rate = 94.6937%

[2021-03-23 16:41:56.490] [jointLog] [info] finished quantifyLibrary()
[2021-03-23 16:41:56.491] [jointLog] [info] Starting optimizer
[2021-03-23 16:41:56.479] [fileLog] [info] 
At end of round 0
==================
Observed 14730503 total fragments (14730503 in most recent round)

[2021-03-23 16:42:00.772] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-23 16:42:01.105] [jointLog] [info] iteration = 0 | max rel diff. = 234.73
[2021-03-23 16:42:04.510] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-23 16:44:02.227] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-23 16:44:02.228] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-23 16:44:13.021] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-23 16:44:23.313] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-23 16:44:34.727] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-23 16:44:45.546] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-23 16:44:56.563] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-23 16:45:07.294] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-23 16:45:18.136] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-23 16:45:28.646] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-23 16:45:39.416] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-23 16:45:50.096] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-23 16:45:50.135] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-23 16:46:22.150] [jointLog] [info] iteration = 100 | max rel diff. = 12.4832
[2021-03-23 16:46:57.415] [jointLog] [info] iteration = 200 | max rel diff. = 2.09411
[2021-03-23 16:47:31.862] [jointLog] [info] iteration = 300 | max rel diff. = 1.03129
[2021-03-23 16:48:06.254] [jointLog] [info] iteration = 400 | max rel diff. = 2.0964
[2021-03-23 16:48:39.393] [jointLog] [info] iteration = 500 | max rel diff. = 0.231014
[2021-03-23 16:49:12.553] [jointLog] [info] iteration = 600 | max rel diff. = 1.01439
[2021-03-23 16:49:45.819] [jointLog] [info] iteration = 700 | max rel diff. = 0.241554
[2021-03-23 16:50:19.805] [jointLog] [info] iteration = 800 | max rel diff. = 0.0444347
[2021-03-23 16:50:53.698] [jointLog] [info] iteration = 900 | max rel diff. = 0.57985
[2021-03-23 16:51:27.435] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.108216
[2021-03-23 16:51:50.741] [jointLog] [info] iteration = 1,070 | max rel diff. = 0.00786761
[2021-03-23 16:51:52.964] [jointLog] [info] Finished optimizer
[2021-03-23 16:51:52.964] [jointLog] [info] writing output