[2021-03-24 09:52:13.973] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-24 09:52:13.973] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-24 09:52:13.973] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-24 09:52:13.973] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-24 09:52:13.973] [jointLog] [info] parsing read library format
[2021-03-24 09:52:13.973] [jointLog] [info] There is 1 library.
[2021-03-24 09:52:14.088] [jointLog] [info] Loading pufferfish index
[2021-03-24 09:52:14.088] [jointLog] [info] Loading dense pufferfish index.
[2021-03-24 09:53:56.296] [jointLog] [info] done
[2021-03-24 09:53:56.296] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-24 09:54:48.396] [jointLog] [info] Number of decoys : 194
[2021-03-24 09:54:48.396] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-24 09:54:49.586] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-24 09:54:49.921] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-24 09:56:29.969] [jointLog] [info] Computed 371,235 rich equivalence classes for further processing
[2021-03-24 09:56:29.969] [jointLog] [info] Counted 15,709,793 total reads in the equivalence classes 
[2021-03-24 09:56:29.979] [jointLog] [info] Number of mappings discarded because of alignment score : 7,507,063
[2021-03-24 09:56:29.979] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 272,977
[2021-03-24 09:56:29.979] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 238,577
[2021-03-24 09:56:29.979] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-24 09:56:29.979] [jointLog] [info] Mapping rate = 96.9415%

[2021-03-24 09:56:29.979] [jointLog] [info] finished quantifyLibrary()
[2021-03-24 09:56:29.979] [jointLog] [info] Starting optimizer
[2021-03-24 09:56:29.970] [fileLog] [info] 
At end of round 0
==================
Observed 16205437 total fragments (16205437 in most recent round)

[2021-03-24 09:56:34.629] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-24 09:56:34.974] [jointLog] [info] iteration = 0 | max rel diff. = 271.894
[2021-03-24 09:56:38.377] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-24 09:58:26.709] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-24 09:58:26.709] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-24 09:58:36.425] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-24 09:58:46.641] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-24 09:58:57.124] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-24 09:59:07.709] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-24 09:59:17.918] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-24 09:59:27.546] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-24 09:59:37.567] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-24 09:59:47.918] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-24 09:59:57.728] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-24 10:00:07.647] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-24 10:00:58.261] [jointLog] [info] iteration = 100 | max rel diff. = 13.7116
[2021-03-24 10:01:36.532] [jointLog] [info] iteration = 200 | max rel diff. = 11.7915
[2021-03-24 10:02:12.177] [jointLog] [info] iteration = 300 | max rel diff. = 0.924429
[2021-03-24 10:03:04.793] [jointLog] [info] iteration = 400 | max rel diff. = 0.15089
[2021-03-24 10:03:37.967] [jointLog] [info] iteration = 500 | max rel diff. = 2.21181
[2021-03-24 10:04:11.196] [jointLog] [info] iteration = 600 | max rel diff. = 1.00002
[2021-03-24 10:04:44.561] [jointLog] [info] iteration = 700 | max rel diff. = 0.50953
[2021-03-24 10:05:17.646] [jointLog] [info] iteration = 800 | max rel diff. = 0.0298264
[2021-03-24 10:05:50.832] [jointLog] [info] iteration = 900 | max rel diff. = 0.0524199
[2021-03-24 10:06:24.179] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.102829
[2021-03-24 10:06:57.090] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0403974
[2021-03-24 10:07:30.387] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0224593
[2021-03-24 10:07:58.485] [jointLog] [info] iteration = 1,286 | max rel diff. = 0.0077647
[2021-03-24 10:08:00.544] [jointLog] [info] Finished optimizer
[2021-03-24 10:08:00.544] [jointLog] [info] writing output