[2022-06-14 23:25:51.073] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-06-14 23:25:51.074] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-06-14 23:25:51.074] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-06-14 23:25:51.074] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-06-14 23:25:51.074] [jointLog] [info] parsing read library format
[2022-06-14 23:25:51.074] [jointLog] [info] There is 1 library.
[2022-06-14 23:25:51.074] [jointLog] [info] Loading pufferfish index
[2022-06-14 23:25:51.074] [jointLog] [info] Loading dense pufferfish index.
[2022-06-14 23:29:19.994] [jointLog] [info] done
[2022-06-14 23:29:20.368] [jointLog] [info] Index contained 5,382,683 targets
[2022-06-14 23:30:59.471] [jointLog] [info] Number of decoys : 194
[2022-06-14 23:30:59.471] [jointLog] [info] First decoy index : 5,185,409 
[2022-06-14 23:31:04.477] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2022-06-14 23:31:07.256] [jointLog] [info] Automatically detected most likely library type as SF

[2022-06-14 23:38:25.168] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments
[2022-06-14 23:38:25.172] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments
[2022-06-14 23:38:25.264] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-06-14 23:38:25.284] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-06-14 23:38:25.303] [jointLog] [info] Thread saw mini-batch with a maximum of 1.26% zero probability fragments
[2022-06-14 23:38:25.662] [jointLog] [info] Thread saw mini-batch with a maximum of 1.26% zero probability fragments
[2022-06-14 23:38:25.683] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-06-14 23:38:26.009] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-06-14 23:38:26.449] [fileLog] [info] 
At end of round 0
==================
Observed 10397878 total fragments (10397878 in most recent round)

[2022-06-14 23:38:26.429] [jointLog] [info] Computed 91,330 rich equivalence classes for further processing
[2022-06-14 23:38:26.429] [jointLog] [info] Counted 5,550,479 total reads in the equivalence classes 
[2022-06-14 23:38:26.456] [jointLog] [info] Number of mappings discarded because of alignment score : 106,601,734
[2022-06-14 23:38:26.456] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,313,650
[2022-06-14 23:38:26.456] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 263,047
[2022-06-14 23:38:26.456] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2022-06-14 23:38:26.456] [jointLog] [info] Mapping rate = 53.3809%

[2022-06-14 23:38:26.456] [jointLog] [info] finished quantifyLibrary()
[2022-06-14 23:38:26.457] [jointLog] [info] Starting optimizer
[2022-06-14 23:38:35.518] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-06-14 23:38:36.358] [jointLog] [info] iteration = 0 | max rel diff. = 99.7914
[2022-06-14 23:38:45.357] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-06-14 23:41:13.454] [jointLog] [info] Computed expected counts (for bias correction)
[2022-06-14 23:41:13.454] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-06-14 23:41:32.843] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-06-14 23:41:48.121] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-06-14 23:42:05.503] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-06-14 23:42:22.304] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-06-14 23:42:39.750] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-06-14 23:42:55.555] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-06-14 23:43:09.605] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-06-14 23:43:25.115] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-06-14 23:43:41.737] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-06-14 23:43:58.120] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-06-14 23:45:17.519] [jointLog] [info] iteration = 100 | max rel diff. = 9.24294
[2022-06-14 23:46:43.202] [jointLog] [info] iteration = 200 | max rel diff. = 1.05142
[2022-06-14 23:48:10.158] [jointLog] [info] iteration = 300 | max rel diff. = 1.45438
[2022-06-14 23:49:37.369] [jointLog] [info] iteration = 400 | max rel diff. = 0.124333
[2022-06-14 23:51:05.142] [jointLog] [info] iteration = 500 | max rel diff. = 0.338529
[2022-06-14 23:52:32.523] [jointLog] [info] iteration = 600 | max rel diff. = 0.956422
[2022-06-14 23:54:03.901] [jointLog] [info] iteration = 700 | max rel diff. = 0.0662551
[2022-06-14 23:55:30.006] [jointLog] [info] iteration = 800 | max rel diff. = 0.05314
[2022-06-14 23:56:55.661] [jointLog] [info] iteration = 900 | max rel diff. = 0.185087
[2022-06-14 23:58:21.206] [jointLog] [info] iteration = 999 | max rel diff. = 0.00711814
[2022-06-14 23:58:24.812] [jointLog] [info] Finished optimizer
[2022-06-14 23:58:24.812] [jointLog] [info] writing output