[2023-10-02 10:38:49.000] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 10:38:49.000] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 10:38:49.000] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 10:38:49.000] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 10:38:49.000] [jointLog] [info] parsing read library format
[2023-10-02 10:38:49.000] [jointLog] [info] There is 1 library.
[2023-10-02 10:38:49.000] [jointLog] [info] Loading pufferfish index
[2023-10-02 10:38:49.000] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 10:40:01.496] [jointLog] [info] done
[2023-10-02 10:40:01.619] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 10:40:38.339] [jointLog] [info] Number of decoys : 194
[2023-10-02 10:40:38.339] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 10:40:39.681] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 10:40:41.051] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 10:40:56.862] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-02 10:40:56.886] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-02 10:40:56.953] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-02 10:40:56.980] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-02 10:40:57.024] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-10-02 10:40:57.107] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-02 10:40:57.192] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-02 10:40:57.281] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-02 10:40:57.408] [jointLog] [info] Computed 59,893 rich equivalence classes for further processing
[2023-10-02 10:40:57.408] [jointLog] [info] Counted 992,442 total reads in the equivalence classes 
[2023-10-02 10:40:57.416] [jointLog] [warning] 7.77036e-05% 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.


[2023-10-02 10:40:57.416] [jointLog] [info] Number of mappings discarded because of alignment score : 10,579,836
[2023-10-02 10:40:57.416] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 69,128
[2023-10-02 10:40:57.416] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 26,027
[2023-10-02 10:40:57.416] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 10:40:57.408] [fileLog] [info] 
At end of round 0
==================
Observed 1286942 total fragments (1286942 in most recent round)

[2023-10-02 10:40:58.577] [jointLog] [warning] Only 992442 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-02 10:40:58.577] [jointLog] [info] Mapping rate = 77.1163%

[2023-10-02 10:40:58.577] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 10:40:58.577] [jointLog] [info] Starting optimizer
[2023-10-02 10:41:03.661] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 10:41:03.976] [jointLog] [info] iteration = 0 | max rel diff. = 18.8397
[2023-10-02 10:41:07.167] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 10:41:47.549] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 10:41:47.549] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 10:41:51.528] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 10:41:55.254] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 10:41:58.889] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 10:42:02.815] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 10:42:06.473] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 10:42:10.276] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 10:42:14.179] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 10:42:17.992] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 10:42:21.911] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 10:42:26.149] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 10:42:57.393] [jointLog] [info] iteration = 100 | max rel diff. = 1.74081
[2023-10-02 10:43:29.726] [jointLog] [info] iteration = 200 | max rel diff. = 0.360317
[2023-10-02 10:44:05.827] [jointLog] [info] iteration = 300 | max rel diff. = 0.254387
[2023-10-02 10:44:40.404] [jointLog] [info] iteration = 400 | max rel diff. = 0.0973627
[2023-10-02 10:45:13.229] [jointLog] [info] iteration = 500 | max rel diff. = 0.025578
[2023-10-02 10:45:47.425] [jointLog] [info] iteration = 600 | max rel diff. = 0.0524638
[2023-10-02 10:46:02.570] [jointLog] [info] iteration = 648 | max rel diff. = 0.000814531
[2023-10-02 10:46:04.391] [jointLog] [info] Finished optimizer
[2023-10-02 10:46:04.391] [jointLog] [info] writing output