[2023-09-01 19:27:26.877] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-01 19:27:26.877] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-01 19:27:26.877] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-01 19:27:26.877] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-01 19:27:26.877] [jointLog] [info] parsing read library format
[2023-09-01 19:27:26.877] [jointLog] [info] There is 1 library.
[2023-09-01 19:27:26.878] [jointLog] [info] Loading pufferfish index
[2023-09-01 19:27:26.878] [jointLog] [info] Loading dense pufferfish index.
[2023-09-01 19:28:44.349] [jointLog] [info] done
[2023-09-01 19:28:44.493] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-01 19:29:24.764] [jointLog] [info] Number of decoys : 194
[2023-09-01 19:29:24.764] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-01 19:29:28.499] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-01 19:39:29.578] [jointLog] [info] Thread saw mini-batch with a maximum of 7.86% zero probability fragments
[2023-09-01 19:39:29.682] [jointLog] [info] Thread saw mini-batch with a maximum of 8.04% zero probability fragments
[2023-09-01 19:39:29.701] [jointLog] [info] Thread saw mini-batch with a maximum of 7.86% zero probability fragments
[2023-09-01 19:39:29.715] [jointLog] [info] Thread saw mini-batch with a maximum of 7.94% zero probability fragments
[2023-09-01 19:39:29.754] [jointLog] [info] Thread saw mini-batch with a maximum of 7.82% zero probability fragments
[2023-09-01 19:39:29.756] [jointLog] [info] Thread saw mini-batch with a maximum of 7.82% zero probability fragments
[2023-09-01 19:39:29.877] [jointLog] [info] Thread saw mini-batch with a maximum of 7.80% zero probability fragments
[2023-09-01 19:39:29.882] [jointLog] [info] Thread saw mini-batch with a maximum of 7.98% zero probability fragments
[2023-09-01 19:39:30.408] [jointLog] [info] Computed 428,151 rich equivalence classes for further processing
[2023-09-01 19:39:30.408] [jointLog] [info] Counted 35,261,806 total reads in the equivalence classes 
[2023-09-01 19:39:30.415] [jointLog] [info] Number of mappings discarded because of alignment score : 27,059,178
[2023-09-01 19:39:30.415] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,919,033
[2023-09-01 19:39:30.415] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 2,394,778
[2023-09-01 19:39:30.415] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,242,814
[2023-09-01 19:39:30.415] [jointLog] [info] Mapping rate = 81.2982%

[2023-09-01 19:39:30.415] [jointLog] [info] finished quantifyLibrary()
[2023-09-01 19:39:30.415] [jointLog] [info] Starting optimizer
[2023-09-01 19:39:30.408] [fileLog] [info] 
At end of round 0
==================
Observed 43373433 total fragments (43373433 in most recent round)

[2023-09-01 19:39:35.922] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-01 19:39:36.313] [jointLog] [info] iteration = 0 | max rel diff. = 332.866
[2023-09-01 19:39:40.199] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-01 19:42:40.119] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-01 19:42:40.120] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-01 19:42:55.317] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-01 19:43:10.933] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-01 19:43:26.502] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-01 19:43:41.661] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-01 19:43:56.625] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-01 19:44:12.129] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-01 19:44:27.931] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-01 19:44:43.086] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-01 19:44:59.038] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-01 19:45:14.417] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-01 19:45:46.286] [jointLog] [info] iteration = 100 | max rel diff. = 19.6674
[2023-09-01 19:46:20.993] [jointLog] [info] iteration = 200 | max rel diff. = 2.22601
[2023-09-01 19:46:56.524] [jointLog] [info] iteration = 300 | max rel diff. = 2.67704
[2023-09-01 19:47:32.018] [jointLog] [info] iteration = 400 | max rel diff. = 7.41389
[2023-09-01 19:48:07.005] [jointLog] [info] iteration = 500 | max rel diff. = 0.203365
[2023-09-01 19:48:42.496] [jointLog] [info] iteration = 600 | max rel diff. = 0.438738
[2023-09-01 19:49:17.696] [jointLog] [info] iteration = 700 | max rel diff. = 0.321413
[2023-09-01 19:49:53.286] [jointLog] [info] iteration = 800 | max rel diff. = 0.0190798
[2023-09-01 19:50:28.378] [jointLog] [info] iteration = 900 | max rel diff. = 0.025998
[2023-09-01 19:51:03.810] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0445511
[2023-09-01 19:51:38.884] [jointLog] [info] iteration = 1,100 | max rel diff. = 7.74317
[2023-09-01 19:51:39.225] [jointLog] [info] iteration = 1,102 | max rel diff. = 0.0026988
[2023-09-01 19:51:41.009] [jointLog] [info] Finished optimizer
[2023-09-01 19:51:41.009] [jointLog] [info] writing output