[2021-04-08 16:05:35.472] [puff::index::jointLog] [info] Running fixFasta
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631435.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000415118.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000448914.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000434970.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632684.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000439842.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390567.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000452198.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390569.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000437320.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390571.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390572.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390574.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390575.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000431870.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000450276.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390578.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000451044.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390580.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390581.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000431440.2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390583.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633210.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000603693.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604838.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604446.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000604102.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000603935.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632524.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633009.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634070.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632963.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633030.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633765.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632619.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631871.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633010.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633159.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632473.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631884.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632859.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631895.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634154.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632609.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632911.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633504.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632304.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000632542.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633968.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000634085.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000633353.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000631803.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.481] [puff::index::jointLog] [warning] Entry with header [ENST00000390584.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390585.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000430425.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000454691.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390588.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000414852.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390590.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000390591.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000454908.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000604642.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000603326.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000604950.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000603077.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:35.482] [puff::index::jointLog] [warning] Entry with header [ENST00000605284.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:36.177] [puff::index::jointLog] [warning] Entry with header [ENST00000629250.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:36.802] [puff::index::jointLog] [warning] Entry with header [ENST00000632054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:37.153] [puff::index::jointLog] [warning] Entry with header [ENST00000437226.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:39.029] [puff::index::jointLog] [warning] Entry with header [ENST00000626807.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:41.767] [puff::index::jointLog] [warning] Entry with header [ENST00000417283.5], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:41.767] [puff::index::jointLog] [warning] Entry with header [ENST00000465958.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.743] [puff::index::jointLog] [warning] Entry with header [ENST00000632342.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.744] [puff::index::jointLog] [warning] Entry with header [ENST00000518246.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.921] [puff::index::jointLog] [warning] Entry with header [ENST00000543745.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:43.944] [puff::index::jointLog] [warning] Entry with header [ENST00000473810.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.105] [puff::index::jointLog] [warning] Entry with header [ENST00000579054.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.116] [puff::index::jointLog] [warning] Entry with header [ENST00000603775.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.236] [puff::index::jointLog] [warning] Entry with header [ENST00000573437.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.251] [puff::index::jointLog] [warning] Entry with header [ENST00000634174.1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2021-04-08 16:05:44.259] [puff::index::jointLog] [warning] Removed 11698 transcripts that were sequence duplicates of indexed transcripts.
[2021-04-08 16:05:44.259] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2021-04-08 16:05:44.355] [puff::index::jointLog] [info] Replaced 5 non-ATCG nucleotides
[2021-04-08 16:05:44.355] [puff::index::jointLog] [info] Clipped poly-A tails from 1439 transcripts
[2021-04-08 16:05:47.703] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2021-04-08 16:05:50.376] [puff::index::jointLog] [info] ntHll estimated 108822814 distinct k-mers, setting filter size to 2^31
[2021-04-08 16:57:20.748] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2021-04-08 16:57:20.749] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory /project/shefflab/deploy/rg.databio.org_full/genomes/data/9a02d64909100f146272f8e16563178e9e93c218b1126ff9/salmon_index/default
[2021-04-08 16:57:21.019] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2021-04-08 16:57:21.028] [puff::index::jointLog] [info] contig count for validation: 1102892
[2021-04-08 16:57:21.474] [puff::index::jointLog] [info] Total # of Contigs : 1102892
[2021-04-08 16:57:21.474] [puff::index::jointLog] [info] Total # of numerical Contigs : 1102892
[2021-04-08 16:57:21.544] [puff::index::jointLog] [info] Total # of contig vec entries: 6373539
[2021-04-08 16:57:21.544] [puff::index::jointLog] [info] bits per offset entry 23
[2021-04-08 16:57:21.879] [puff::index::jointLog] [info] Done constructing the contig vector. 1102893
[2021-04-08 16:57:22.642] [puff::index::jointLog] [info] # segments = 1102892
[2021-04-08 16:57:22.642] [puff::index::jointLog] [info] total length = 142900026
[2021-04-08 16:57:22.705] [puff::index::jointLog] [info] Reading the reference files ...
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] positional integer width = 28
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] seqSize = 142900026
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] rankSize = 142900026
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] edgeVecSize = 0
[2021-04-08 16:57:24.389] [puff::index::jointLog] [info] num keys = 109813266
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] mphf size = 68.5921 MB
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk size = 17862504
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 0 = [0, 17862504)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 1 = [17862504, 35725008)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 2 = [35725008, 53587534)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 3 = [53587534, 71450054)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 4 = [71450054, 89312558)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 5 = [89312558, 107175062)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 6 = [107175062, 125037580)
[2021-04-08 16:57:44.417] [puff::index::jointLog] [info] chunk 7 = [125037580, 142899996)
[2021-04-08 16:58:11.814] [puff::index::jointLog] [info] finished populating pos vector
[2021-04-08 16:58:11.814] [puff::index::jointLog] [info] writing index components
[2021-04-08 16:58:13.958] [puff::index::jointLog] [info] finished writing dense pufferfish index