[2023-10-05 06:00:03.977] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 06:00:03.977] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 06:00:03.977] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 06:00:03.977] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 06:00:03.977] [jointLog] [info] parsing read library format
[2023-10-05 06:00:03.977] [jointLog] [info] There is 1 library.
[2023-10-05 06:00:03.978] [jointLog] [info] Loading pufferfish index
[2023-10-05 06:00:03.978] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 06:01:21.475] [jointLog] [info] done
[2023-10-05 06:01:21.602] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 06:01:59.182] [jointLog] [info] Number of decoys : 194
[2023-10-05 06:01:59.182] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 06:02:00.935] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 06:02:01.837] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 06:02:24.705] [jointLog] [info] Thread saw mini-batch with a maximum of 2.76% zero probability fragments
[2023-10-05 06:02:24.727] [jointLog] [info] Thread saw mini-batch with a maximum of 2.66% zero probability fragments
[2023-10-05 06:02:24.823] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-05 06:02:24.842] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-10-05 06:02:24.885] [jointLog] [info] Thread saw mini-batch with a maximum of 3.04% zero probability fragments
[2023-10-05 06:02:24.952] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-05 06:02:24.972] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-10-05 06:02:25.009] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-05 06:02:25.149] [jointLog] [info] Computed 58,289 rich equivalence classes for further processing
[2023-10-05 06:02:25.149] [jointLog] [info] Counted 1,414,228 total reads in the equivalence classes 
[2023-10-05 06:02:25.156] [jointLog] [warning] 0.000106801% 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.


[2023-10-05 06:02:25.156] [jointLog] [info] Number of mappings discarded because of alignment score : 26,058,269
[2023-10-05 06:02:25.156] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 179,703
[2023-10-05 06:02:25.156] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 50,308
[2023-10-05 06:02:25.156] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 06:02:25.150] [fileLog] [info] 
At end of round 0
==================
Observed 1872635 total fragments (1872635 in most recent round)

[2023-10-05 06:02:26.430] [jointLog] [warning] Only 1414228 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 06:02:26.430] [jointLog] [info] Mapping rate = 75.5208%

[2023-10-05 06:02:26.430] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 06:02:26.430] [jointLog] [info] Starting optimizer
[2023-10-05 06:02:30.785] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 06:02:31.116] [jointLog] [info] iteration = 0 | max rel diff. = 27.6344
[2023-10-05 06:02:34.522] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 06:03:12.952] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 06:03:12.953] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 06:03:16.158] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 06:03:19.582] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 06:03:23.160] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 06:03:26.506] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 06:03:30.022] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 06:03:33.525] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 06:03:37.113] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 06:03:40.434] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 06:03:44.273] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 06:03:47.757] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 06:04:17.682] [jointLog] [info] iteration = 100 | max rel diff. = 5.3337
[2023-10-05 06:04:50.265] [jointLog] [info] iteration = 200 | max rel diff. = 0.771509
[2023-10-05 06:05:22.742] [jointLog] [info] iteration = 300 | max rel diff. = 1.59707
[2023-10-05 06:05:55.231] [jointLog] [info] iteration = 400 | max rel diff. = 0.0563064
[2023-10-05 06:06:28.507] [jointLog] [info] iteration = 500 | max rel diff. = 0.830217
[2023-10-05 06:07:01.949] [jointLog] [info] iteration = 600 | max rel diff. = 0.0150659
[2023-10-05 06:07:35.053] [jointLog] [info] iteration = 700 | max rel diff. = 0.122409
[2023-10-05 06:07:38.019] [jointLog] [info] iteration = 710 | max rel diff. = 0.00837131
[2023-10-05 06:07:39.829] [jointLog] [info] Finished optimizer
[2023-10-05 06:07:39.829] [jointLog] [info] writing output