[2020-04-30 07:03:52.664] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:52.664] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:52.664] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:52.664] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:52.664] [jointLog] [info] parsing read library format [2020-04-30 07:03:52.664] [jointLog] [info] There is 1 library. [2020-04-30 07:03:52.733] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:52.733] [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 07:03:52.733] [jointLog] [info] Loading dense pufferfish index. [2020-04-30 07:03:52.858] [jointLog] [info] done [2020-04-30 07:03:52.858] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:52.875] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:53.505] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:04:01.774] [jointLog] [info] Computed 24,349 rich equivalence classes for further processing [2020-04-30 07:04:01.774] [jointLog] [info] Counted 3,167,685 total reads in the equivalence classes [2020-04-30 07:04:01.786] [jointLog] [info] Number of mappings discarded because of alignment score : 719,234 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,412 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,235 [2020-04-30 07:04:01.789] [jointLog] [warning] Only 3167685 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 07:04:01.789] [jointLog] [info] Mapping rate = 99.2983% [2020-04-30 07:04:01.789] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:01.790] [jointLog] [info] Starting optimizer [2020-04-30 07:04:01.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:01.807] [jointLog] [info] iteration = 0 | max rel diff. = 6601.82 [2020-04-30 07:04:01.775] [fileLog] [info] At end of round 0 ================== Observed 3190071 total fragments (3190071 in most recent round) [2020-04-30 07:04:01.899] [jointLog] [info] iteration = 100 | max rel diff. = 9.58813 [2020-04-30 07:04:01.978] [jointLog] [info] iteration = 200 | max rel diff. = 3.33627 [2020-04-30 07:04:02.053] [jointLog] [info] iteration = 300 | max rel diff. = 0.302549 [2020-04-30 07:04:02.127] [jointLog] [info] iteration = 400 | max rel diff. = 2.87797 [2020-04-30 07:04:02.200] [jointLog] [info] iteration = 500 | max rel diff. = 0.357354 [2020-04-30 07:04:02.270] [jointLog] [info] iteration = 596 | max rel diff. = 0.0028829 [2020-04-30 07:04:02.271] [jointLog] [info] Finished optimizer [2020-04-30 07:04:02.271] [jointLog] [info] writing output