[2021-03-24 04:28:12.037] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-24 04:28:12.037] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-24 04:28:12.037] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-24 04:28:12.037] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-24 04:28:12.037] [jointLog] [info] parsing read library format
[2021-03-24 04:28:12.037] [jointLog] [info] There is 1 library.
[2021-03-24 04:28:12.113] [jointLog] [info] Loading pufferfish index
[2021-03-24 04:28:12.113] [jointLog] [info] Loading dense pufferfish index.
[2021-03-24 04:29:55.034] [jointLog] [info] done
[2021-03-24 04:29:55.034] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-24 04:30:52.052] [jointLog] [info] Number of decoys : 194
[2021-03-24 04:30:52.052] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-24 04:30:53.446] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-24 04:30:53.936] [jointLog] [info] Automatically detected most likely library type as U
[2021-03-24 04:32:21.669] [fileLog] [info] 
At end of round 0
==================
Observed 13693228 total fragments (13693228 in most recent round)

[2021-03-24 04:32:21.668] [jointLog] [info] Computed 352,219 rich equivalence classes for further processing
[2021-03-24 04:32:21.668] [jointLog] [info] Counted 13,283,114 total reads in the equivalence classes 
[2021-03-24 04:32:21.708] [jointLog] [info] Number of mappings discarded because of alignment score : 6,155,762
[2021-03-24 04:32:21.708] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 224,327
[2021-03-24 04:32:21.708] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 193,371
[2021-03-24 04:32:21.708] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-24 04:32:21.708] [jointLog] [info] Mapping rate = 97.005%

[2021-03-24 04:32:21.708] [jointLog] [info] finished quantifyLibrary()
[2021-03-24 04:32:21.708] [jointLog] [info] Starting optimizer
[2021-03-24 04:32:27.434] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-24 04:32:27.784] [jointLog] [info] iteration = 0 | max rel diff. = 249.5
[2021-03-24 04:32:31.329] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-24 04:34:21.487] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-24 04:34:21.488] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-24 04:34:31.445] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-24 04:34:41.483] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-24 04:34:51.987] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-24 04:35:02.418] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-24 04:35:12.673] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-24 04:35:23.025] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-24 04:35:33.253] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-24 04:35:43.497] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-24 04:35:53.595] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-24 04:36:03.441] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-24 04:36:36.368] [jointLog] [info] iteration = 100 | max rel diff. = 9.67445
[2021-03-24 04:37:10.856] [jointLog] [info] iteration = 200 | max rel diff. = 6.83351
[2021-03-24 04:37:45.146] [jointLog] [info] iteration = 300 | max rel diff. = 1.40934
[2021-03-24 04:38:19.097] [jointLog] [info] iteration = 400 | max rel diff. = 1.52551
[2021-03-24 04:38:52.865] [jointLog] [info] iteration = 500 | max rel diff. = 0.290246
[2021-03-24 04:39:27.055] [jointLog] [info] iteration = 600 | max rel diff. = 0.228026
[2021-03-24 04:40:00.481] [jointLog] [info] iteration = 700 | max rel diff. = 4.7082
[2021-03-24 04:40:33.534] [jointLog] [info] iteration = 800 | max rel diff. = 0.333526
[2021-03-24 04:41:07.100] [jointLog] [info] iteration = 900 | max rel diff. = 0.249034
[2021-03-24 04:41:40.702] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.987616
[2021-03-24 04:42:14.333] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.256969
[2021-03-24 04:42:19.759] [jointLog] [info] iteration = 1,117 | max rel diff. = 0.0068139
[2021-03-24 04:42:21.994] [jointLog] [info] Finished optimizer
[2021-03-24 04:42:21.994] [jointLog] [info] writing output