[2023-10-05 08:04:00.667] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 08:04:00.667] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 08:04:00.667] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 08:04:00.667] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 08:04:00.667] [jointLog] [info] parsing read library format
[2023-10-05 08:04:00.667] [jointLog] [info] There is 1 library.
[2023-10-05 08:04:00.667] [jointLog] [info] Loading pufferfish index
[2023-10-05 08:04:00.668] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 08:05:18.452] [jointLog] [info] done
[2023-10-05 08:05:18.592] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 08:05:56.937] [jointLog] [info] Number of decoys : 194
[2023-10-05 08:05:56.937] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 08:05:58.650] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 08:05:59.544] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 08:06:41.288] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-05 08:06:41.345] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-05 08:06:41.379] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-10-05 08:06:41.381] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-05 08:06:41.502] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-05 08:06:41.634] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-05 08:06:41.644] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-05 08:06:41.714] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-05 08:06:41.871] [jointLog] [info] Computed 74,342 rich equivalence classes for further processing
[2023-10-05 08:06:41.871] [jointLog] [info] Counted 2,481,175 total reads in the equivalence classes 
[2023-10-05 08:06:41.879] [jointLog] [info] Number of mappings discarded because of alignment score : 36,610,634
[2023-10-05 08:06:41.879] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 237,237
[2023-10-05 08:06:41.879] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 73,837
[2023-10-05 08:06:41.879] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 08:06:41.872] [fileLog] [info] 
At end of round 0
==================
Observed 3361027 total fragments (3361027 in most recent round)

[2023-10-05 08:06:42.959] [jointLog] [warning] Only 2481175 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 08:06:42.959] [jointLog] [info] Mapping rate = 73.8219%

[2023-10-05 08:06:42.959] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 08:06:42.960] [jointLog] [info] Starting optimizer
[2023-10-05 08:06:47.566] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 08:06:47.906] [jointLog] [info] iteration = 0 | max rel diff. = 54.7168
[2023-10-05 08:06:51.317] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 08:07:42.587] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 08:07:42.587] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 08:07:46.624] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 08:07:51.100] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 08:07:56.052] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 08:08:00.970] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 08:08:05.853] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 08:08:10.652] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 08:08:15.113] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 08:08:19.547] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 08:08:24.443] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 08:08:28.671] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 08:08:58.752] [jointLog] [info] iteration = 100 | max rel diff. = 20.6169
[2023-10-05 08:09:32.448] [jointLog] [info] iteration = 200 | max rel diff. = 0.538427
[2023-10-05 08:10:06.343] [jointLog] [info] iteration = 300 | max rel diff. = 0.0533522
[2023-10-05 08:10:39.853] [jointLog] [info] iteration = 400 | max rel diff. = 0.358459
[2023-10-05 08:11:13.126] [jointLog] [info] iteration = 500 | max rel diff. = 0.427105
[2023-10-05 08:11:46.551] [jointLog] [info] iteration = 600 | max rel diff. = 1.17341
[2023-10-05 08:11:49.896] [jointLog] [info] iteration = 611 | max rel diff. = 0.0096618
[2023-10-05 08:11:52.171] [jointLog] [info] Finished optimizer
[2023-10-05 08:11:52.171] [jointLog] [info] writing output