[2023-09-29 16:13:32.427] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-29 16:13:32.427] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-29 16:13:32.427] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-29 16:13:32.427] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-29 16:13:32.427] [jointLog] [info] parsing read library format
[2023-09-29 16:13:32.427] [jointLog] [info] There is 1 library.
[2023-09-29 16:13:32.427] [jointLog] [info] Loading pufferfish index
[2023-09-29 16:13:32.427] [jointLog] [info] Loading dense pufferfish index.
[2023-09-29 16:14:48.594] [jointLog] [info] done
[2023-09-29 16:14:48.722] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-29 16:15:25.474] [jointLog] [info] Number of decoys : 194
[2023-09-29 16:15:25.474] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-29 16:15:26.711] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-29 16:15:27.534] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-29 16:15:50.715] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-09-29 16:15:50.787] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-09-29 16:15:50.792] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-09-29 16:15:50.802] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-29 16:15:50.872] [jointLog] [info] Thread saw mini-batch with a maximum of 3.14% zero probability fragments
[2023-09-29 16:15:50.900] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-09-29 16:15:50.969] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-09-29 16:15:51.085] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-09-29 16:15:51.243] [jointLog] [info] Computed 71,095 rich equivalence classes for further processing
[2023-09-29 16:15:51.243] [jointLog] [info] Counted 1,522,394 total reads in the equivalence classes 
[2023-09-29 16:15:51.255] [jointLog] [warning] 0.000102506% 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 10.


[2023-09-29 16:15:51.255] [jointLog] [info] Number of mappings discarded because of alignment score : 20,614,646
[2023-09-29 16:15:51.255] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 120,190
[2023-09-29 16:15:51.255] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 44,480
[2023-09-29 16:15:51.255] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-29 16:15:51.244] [fileLog] [info] 
At end of round 0
==================
Observed 1951110 total fragments (1951110 in most recent round)

[2023-09-29 16:15:52.134] [jointLog] [warning] Only 1522394 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-29 16:15:52.134] [jointLog] [info] Mapping rate = 78.0271%

[2023-09-29 16:15:52.134] [jointLog] [info] finished quantifyLibrary()
[2023-09-29 16:15:52.135] [jointLog] [info] Starting optimizer
[2023-09-29 16:15:56.334] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-29 16:15:56.661] [jointLog] [info] iteration = 0 | max rel diff. = 31.6121
[2023-09-29 16:15:59.915] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-29 16:16:46.172] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-29 16:16:46.172] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-29 16:16:50.422] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-29 16:16:54.603] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-29 16:16:58.901] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-29 16:17:03.415] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-29 16:17:07.792] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-29 16:17:12.416] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-29 16:17:16.758] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-29 16:17:21.360] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-29 16:17:25.983] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-29 16:17:29.955] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-29 16:17:58.181] [jointLog] [info] iteration = 100 | max rel diff. = 3.46423
[2023-09-29 16:18:29.724] [jointLog] [info] iteration = 200 | max rel diff. = 0.491254
[2023-09-29 16:19:01.385] [jointLog] [info] iteration = 300 | max rel diff. = 0.737779
[2023-09-29 16:19:32.615] [jointLog] [info] iteration = 400 | max rel diff. = 0.0792985
[2023-09-29 16:19:37.368] [jointLog] [info] iteration = 416 | max rel diff. = 0.00576627
[2023-09-29 16:19:39.083] [jointLog] [info] Finished optimizer
[2023-09-29 16:19:39.083] [jointLog] [info] writing output