[2020-04-30 07:03:03.475] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:03.475] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:03.475] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:03.475] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:03.475] [jointLog] [info] parsing read library format [2020-04-30 07:03:03.475] [jointLog] [info] There is 1 library. [2020-04-30 07:03:03.543] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:03.544] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:03.544] [jointLog] [info] Loading dense pufferfish index. [2020-04-30 07:03:03.656] [jointLog] [info] done [2020-04-30 07:03:03.656] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:03.673] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:04.368] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:03:14.268] [jointLog] [info] Computed 26,039 rich equivalence classes for further processing [2020-04-30 07:03:14.268] [jointLog] [info] Counted 3,189,366 total reads in the equivalence classes [2020-04-30 07:03:14.280] [jointLog] [info] Number of mappings discarded because of alignment score : 981,336 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,429 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,120 [2020-04-30 07:03:14.283] [jointLog] [warning] Only 3189366 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:14.283] [jointLog] [info] Mapping rate = 99.2371% [2020-04-30 07:03:14.283] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:14.284] [jointLog] [info] Starting optimizer [2020-04-30 07:03:14.299] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:14.301] [jointLog] [info] iteration = 0 | max rel diff. = 7375.34 [2020-04-30 07:03:14.399] [jointLog] [info] iteration = 100 | max rel diff. = 14.9726 [2020-04-30 07:03:14.483] [jointLog] [info] iteration = 200 | max rel diff. = 0.237581 [2020-04-30 07:03:14.562] [jointLog] [info] iteration = 300 | max rel diff. = 0.312664 [2020-04-30 07:03:14.641] [jointLog] [info] iteration = 400 | max rel diff. = 0.177105 [2020-04-30 07:03:14.269] [fileLog] [info] At end of round 0 ================== Observed 3213886 total fragments (3213886 in most recent round) [2020-04-30 07:03:14.720] [jointLog] [info] iteration = 500 | max rel diff. = 0.0780449 [2020-04-30 07:03:14.773] [jointLog] [info] iteration = 568 | max rel diff. = 0.0086786 [2020-04-30 07:03:14.774] [jointLog] [info] Finished optimizer [2020-04-30 07:03:14.774] [jointLog] [info] writing output