[2023-09-08 17:23:15.362] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-08 17:23:15.362] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-08 17:23:15.362] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-08 17:23:15.362] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-08 17:23:15.362] [jointLog] [info] parsing read library format
[2023-09-08 17:23:15.362] [jointLog] [info] There is 1 library.
[2023-09-08 17:23:15.363] [jointLog] [info] Loading pufferfish index
[2023-09-08 17:23:15.363] [jointLog] [info] Loading dense pufferfish index.
[2023-09-08 17:24:32.079] [jointLog] [info] done
[2023-09-08 17:24:32.196] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-08 17:25:12.054] [jointLog] [info] Number of decoys : 194
[2023-09-08 17:25:12.054] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-08 17:25:15.588] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-09-08 17:35:16.318] [jointLog] [info] Thread saw mini-batch with a maximum of 6.54% zero probability fragments
[2023-09-08 17:35:16.324] [jointLog] [info] Thread saw mini-batch with a maximum of 6.28% zero probability fragments
[2023-09-08 17:35:16.511] [jointLog] [info] Thread saw mini-batch with a maximum of 6.32% zero probability fragments
[2023-09-08 17:35:16.614] [jointLog] [info] Thread saw mini-batch with a maximum of 6.40% zero probability fragments
[2023-09-08 17:35:16.653] [jointLog] [info] Thread saw mini-batch with a maximum of 6.34% zero probability fragments
[2023-09-08 17:35:16.660] [jointLog] [info] Thread saw mini-batch with a maximum of 6.38% zero probability fragments
[2023-09-08 17:35:16.716] [jointLog] [info] Thread saw mini-batch with a maximum of 6.20% zero probability fragments
[2023-09-08 17:35:16.744] [jointLog] [info] Thread saw mini-batch with a maximum of 6.38% zero probability fragments
[2023-09-08 17:35:17.473] [fileLog] [info] 
At end of round 0
==================
Observed 40277979 total fragments (40277979 in most recent round)

[2023-09-08 17:35:17.472] [jointLog] [info] Computed 331,054 rich equivalence classes for further processing
[2023-09-08 17:35:17.472] [jointLog] [info] Counted 33,516,200 total reads in the equivalence classes 
[2023-09-08 17:35:17.482] [jointLog] [warning] 0.000260688% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 30.


[2023-09-08 17:35:17.482] [jointLog] [info] Number of mappings discarded because of alignment score : 10,311,442
[2023-09-08 17:35:17.482] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,944,499
[2023-09-08 17:35:17.482] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 3,113,317
[2023-09-08 17:35:17.482] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,018,673
[2023-09-08 17:35:17.482] [jointLog] [info] Mapping rate = 83.2122%

[2023-09-08 17:35:17.482] [jointLog] [info] finished quantifyLibrary()
[2023-09-08 17:35:17.483] [jointLog] [info] Starting optimizer
[2023-09-08 17:35:22.867] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-08 17:35:23.221] [jointLog] [info] iteration = 0 | max rel diff. = 261.013
[2023-09-08 17:35:26.754] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-08 17:41:06.621] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-08 17:41:06.621] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-08 17:41:34.251] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-08 17:42:03.733] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-08 17:42:31.088] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-08 17:42:57.748] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-08 17:43:24.889] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-08 17:43:51.728] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-08 17:44:18.470] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-08 17:44:45.020] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-08 17:45:10.524] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-08 17:45:38.970] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-08 17:46:10.714] [jointLog] [info] iteration = 100 | max rel diff. = 13.8581
[2023-09-08 17:46:45.744] [jointLog] [info] iteration = 200 | max rel diff. = 4.59603
[2023-09-08 17:47:20.899] [jointLog] [info] iteration = 300 | max rel diff. = 7.75933
[2023-09-08 17:47:55.565] [jointLog] [info] iteration = 400 | max rel diff. = 0.948697
[2023-09-08 17:48:30.546] [jointLog] [info] iteration = 500 | max rel diff. = 0.123236
[2023-09-08 17:49:05.723] [jointLog] [info] iteration = 600 | max rel diff. = 0.552211
[2023-09-08 17:49:39.414] [jointLog] [info] iteration = 700 | max rel diff. = 0.0474822
[2023-09-08 17:50:12.995] [jointLog] [info] iteration = 800 | max rel diff. = 0.10377
[2023-09-08 17:50:46.903] [jointLog] [info] iteration = 900 | max rel diff. = 0.615757
[2023-09-08 17:51:20.885] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.653135
[2023-09-08 17:51:54.846] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.349221
[2023-09-08 17:52:23.994] [jointLog] [info] iteration = 1,188 | max rel diff. = 0.00662051
[2023-09-08 17:52:26.200] [jointLog] [info] Finished optimizer
[2023-09-08 17:52:26.200] [jointLog] [info] writing output