[2022-12-20 23:46:13.152] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:46:13.152] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:46:13.152] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:46:13.152] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:46:13.152] [jointLog] [info] parsing read library format
[2022-12-20 23:46:13.152] [jointLog] [info] There is 1 library.
[2022-12-20 23:46:13.152] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:46:13.152] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:46:37.664] [jointLog] [info] done
[2022-12-20 23:46:37.701] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:46:37.982] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:46:37.982] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:46:38.747] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:51:10.840] [jointLog] [info] Thread saw mini-batch with a maximum of 0.34% zero probability fragments
[2022-12-20 23:51:11.001] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:51:11.008] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:51:11.042] [jointLog] [info] Thread saw mini-batch with a maximum of 0.30% zero probability fragments
[2022-12-20 23:51:11.106] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:51:11.181] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:51:11.235] [jointLog] [info] Thread saw mini-batch with a maximum of 0.32% zero probability fragments
[2022-12-20 23:51:11.297] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:51:11.559] [fileLog] [info] 
At end of round 0
==================
Observed 20207001 total fragments (20207001 in most recent round)

[2022-12-20 23:51:11.559] [jointLog] [info] Computed 270,511 rich equivalence classes for further processing
[2022-12-20 23:51:11.559] [jointLog] [info] Counted 15,120,995 total reads in the equivalence classes 
[2022-12-20 23:51:11.564] [jointLog] [info] Number of mappings discarded because of alignment score : 41,367,931
[2022-12-20 23:51:11.564] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,076,647
[2022-12-20 23:51:11.564] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 312,786
[2022-12-20 23:51:11.564] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,115,202
[2022-12-20 23:51:11.564] [jointLog] [info] Mapping rate = 74.8305%

[2022-12-20 23:51:11.564] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:51:11.581] [jointLog] [info] Starting optimizer
[2022-12-20 23:51:11.681] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:51:11.696] [jointLog] [info] iteration = 0 | max rel diff. = 7007.67
[2022-12-20 23:51:11.841] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:51:13.269] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:51:13.270] [jointLog] [info] processed bias for 0.1% of the transcripts
[2022-12-20 23:51:14.207] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:51:15.225] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:51:16.163] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-20 23:51:17.061] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:51:17.997] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:51:18.847] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:51:19.670] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:51:20.556] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-12-20 23:51:21.532] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:51:22.359] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:51:22.362] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:51:23.673] [jointLog] [info] iteration = 100 | max rel diff. = 20.7732
[2022-12-20 23:51:25.100] [jointLog] [info] iteration = 200 | max rel diff. = 5.16272
[2022-12-20 23:51:26.562] [jointLog] [info] iteration = 300 | max rel diff. = 1.32226
[2022-12-20 23:51:28.011] [jointLog] [info] iteration = 400 | max rel diff. = 0.459557
[2022-12-20 23:51:29.466] [jointLog] [info] iteration = 500 | max rel diff. = 0.257092
[2022-12-20 23:51:30.922] [jointLog] [info] iteration = 600 | max rel diff. = 0.0863527
[2022-12-20 23:51:32.403] [jointLog] [info] iteration = 700 | max rel diff. = 0.0464801
[2022-12-20 23:51:33.869] [jointLog] [info] iteration = 800 | max rel diff. = 0.602338
[2022-12-20 23:51:35.308] [jointLog] [info] iteration = 900 | max rel diff. = 0.0244386
[2022-12-20 23:51:36.828] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0266691
[2022-12-20 23:51:38.267] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.161603
[2022-12-20 23:51:39.748] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0576236
[2022-12-20 23:51:41.190] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0231476
[2022-12-20 23:51:42.640] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.399579
[2022-12-20 23:51:44.072] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0339993
[2022-12-20 23:51:44.552] [jointLog] [info] iteration = 1,534 | max rel diff. = 0.00834054
[2022-12-20 23:51:44.571] [jointLog] [info] Finished optimizer
[2022-12-20 23:51:44.571] [jointLog] [info] writing output