[2020-03-04 13:30:37.221] [puff::index::jointLog] [info] Running fixFasta
[2020-03-04 13:30:39.414] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:39.537] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:39.940] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:41.419] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.305] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-04 13:30:43.387] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.603] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.603] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.603] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.868] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.869] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.870] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.870] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.870] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.870] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.870] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.874] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.874] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.874] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.874] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:43.874] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:44.810] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:45.505] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:46.523] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:46.523] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:46.523] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:46.523] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:30:46.524] [puff::index::jointLog] [error] In FixFasta, two references with the same name but different sequences: EBNA1. We require that all input records have a unique name up to the first whitespace character.
[2020-03-04 13:42:09.210] [puff::index::jointLog] [info] Running fixFasta
[2020-03-04 13:42:11.172] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:11.298] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:11.719] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:12.712] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:14.543] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-04 13:42:14.626] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:14.837] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:14.837] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:14.837] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.109] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.110] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.111] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.112] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.112] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.112] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.112] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.112] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.116] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.116] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.116] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.116] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:15.116] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:16.069] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:16.759] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.802] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.802] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.802] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.802] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.805] [puff::index::jointLog] [warning] Entry with header [miBART-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.805] [puff::index::jointLog] [warning] Entry with header [miBART-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 13:42:17.806] [puff::index::jointLog] [warning] Removed 789 transcripts that were sequence duplicates of indexed transcripts.
[2020-03-04 13:42:17.806] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-03-04 13:42:17.813] [puff::index::jointLog] [info] Replaced 110 non-ATCG nucleotides
[2020-03-04 13:42:17.813] [puff::index::jointLog] [info] Clipped poly-A tails from 1,524 transcripts
[2020-03-04 13:42:19.356] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-03-04 13:42:22.672] [puff::index::jointLog] [info] ntHll estimated 123752566 distinct k-mers, setting filter size to 2^31
[2020-03-04 14:22:06.387] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ref/GRCh38/Sequence/SalmonQuasiIndex/1.1.0/GencodeTranscriptome/25_1
[2020-03-04 14:22:07.055] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-03-04 14:22:07.378] [puff::index::jointLog] [info] contig count for validation: 1224219
[2020-03-04 14:22:08.101] [puff::index::jointLog] [info] Total # of Contigs : 1,224,219
[2020-03-04 14:22:08.101] [puff::index::jointLog] [info] Total # of numerical Contigs : 1,224,219
[2020-03-04 14:22:09.672] [puff::index::jointLog] [info] 
Total # of segments we have position for : 1,224,219
[2020-03-04 14:22:09.832] [puff::index::jointLog] [info] total contig vec entries 6,015,665
[2020-03-04 14:22:09.832] [puff::index::jointLog] [info] bits per offset entry 23
[2020-03-04 14:22:10.861] [puff::index::jointLog] [info] there were 779,113  equivalence classes
[2020-03-04 14:22:13.704] [puff::index::jointLog] [info] # segments = 1,224,219
[2020-03-04 14:22:13.704] [puff::index::jointLog] [info] total length = 161,576,681
[2020-03-04 14:22:13.798] [puff::index::jointLog] [error] Two references with the same name but different sequences: EBNA3B. We require that all input records have a unique name up to the first whitespace character.
[2020-03-04 14:36:55.100] [puff::index::jointLog] [info] Running fixFasta
[2020-03-04 14:36:57.717] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:36:58.172] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:36:58.692] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:36:59.669] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:01.441] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-04 14:37:01.570] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:01.901] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:01.901] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:01.901] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.193] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.194] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.196] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.196] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.196] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.196] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.196] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.198] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.198] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.198] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.198] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:02.198] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:03.109] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:03.770] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.882] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.882] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.882] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.882] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.885] [puff::index::jointLog] [warning] Entry with header [miBART-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.885] [puff::index::jointLog] [warning] Entry with header [miBART-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 14:37:04.886] [puff::index::jointLog] [warning] Removed 789 transcripts that were sequence duplicates of indexed transcripts.
[2020-03-04 14:37:04.886] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-03-04 14:37:04.894] [puff::index::jointLog] [info] Replaced 110 non-ATCG nucleotides
[2020-03-04 14:37:04.894] [puff::index::jointLog] [info] Clipped poly-A tails from 1,524 transcripts
[2020-03-04 14:37:06.454] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-03-04 14:37:09.907] [puff::index::jointLog] [info] ntHll estimated 123752566 distinct k-mers, setting filter size to 2^31
[2020-03-04 15:15:53.248] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ref/GRCh38/Sequence/SalmonQuasiIndex/1.1.0/GencodeTranscriptome/25_1
[2020-03-04 15:15:54.102] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-03-04 15:15:54.452] [puff::index::jointLog] [info] contig count for validation: 1224219
[2020-03-04 15:15:55.316] [puff::index::jointLog] [info] Total # of Contigs : 1,224,219
[2020-03-04 15:15:55.316] [puff::index::jointLog] [info] Total # of numerical Contigs : 1,224,219
[2020-03-04 15:15:57.045] [puff::index::jointLog] [info] 
Total # of segments we have position for : 1,224,219
[2020-03-04 15:15:57.228] [puff::index::jointLog] [info] total contig vec entries 6,015,665
[2020-03-04 15:15:57.228] [puff::index::jointLog] [info] bits per offset entry 23
[2020-03-04 15:15:58.286] [puff::index::jointLog] [info] there were 779,113  equivalence classes
[2020-03-04 15:16:01.460] [puff::index::jointLog] [info] # segments = 1,224,219
[2020-03-04 15:16:01.460] [puff::index::jointLog] [info] total length = 161,576,681
[2020-03-04 15:16:01.554] [puff::index::jointLog] [error] Two references with the same name but different sequences: EBNA3B_1. We require that all input records have a unique name up to the first whitespace character.
[2020-03-04 15:19:28.270] [puff::index::jointLog] [info] Running fixFasta
[2020-03-04 15:19:30.561] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:30.689] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:31.111] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:32.147] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.014] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-04 15:19:34.097] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.311] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.311] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.311] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.586] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.587] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.588] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.588] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.588] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.588] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.588] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.592] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.592] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.592] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.592] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:34.592] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:35.550] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:36.232] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.282] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.282] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.282] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.282] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.285] [puff::index::jointLog] [warning] Entry with header [miBART-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.285] [puff::index::jointLog] [warning] Entry with header [miBART-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 15:19:37.285] [puff::index::jointLog] [warning] Removed 789 transcripts that were sequence duplicates of indexed transcripts.
[2020-03-04 15:19:37.285] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-03-04 15:19:37.296] [puff::index::jointLog] [info] Replaced 110 non-ATCG nucleotides
[2020-03-04 15:19:37.296] [puff::index::jointLog] [info] Clipped poly-A tails from 1,524 transcripts
[2020-03-04 15:19:39.740] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-03-04 15:19:43.335] [puff::index::jointLog] [info] ntHll estimated 123752566 distinct k-mers, setting filter size to 2^31
[2020-03-04 15:56:37.296] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ref/GRCh38/Sequence/SalmonQuasiIndex/1.1.0/GencodeTranscriptome/25_1
[2020-03-04 15:56:38.030] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-03-04 15:56:38.473] [puff::index::jointLog] [info] contig count for validation: 1224219
[2020-03-04 15:56:39.420] [puff::index::jointLog] [info] Total # of Contigs : 1,224,219
[2020-03-04 15:56:39.420] [puff::index::jointLog] [info] Total # of numerical Contigs : 1,224,219
[2020-03-04 15:56:41.542] [puff::index::jointLog] [info] 
Total # of segments we have position for : 1,224,219
[2020-03-04 15:56:41.737] [puff::index::jointLog] [info] total contig vec entries 6,015,665
[2020-03-04 15:56:41.737] [puff::index::jointLog] [info] bits per offset entry 23
[2020-03-04 15:56:43.142] [puff::index::jointLog] [info] there were 779,113  equivalence classes
[2020-03-04 15:56:46.212] [puff::index::jointLog] [info] # segments = 1,224,219
[2020-03-04 15:56:46.212] [puff::index::jointLog] [info] total length = 161,576,681
[2020-03-04 15:56:46.308] [puff::index::jointLog] [error] Two references with the same name but different sequences: EBNA3B_CDS. We require that all input records have a unique name up to the first whitespace character.
[2020-03-04 16:01:54.520] [puff::index::jointLog] [info] Running fixFasta
[2020-03-04 16:01:56.808] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:56.915] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:57.275] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:58.149] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:59.738] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-04 16:01:59.809] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:59.996] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:59.996] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:01:59.996] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.228] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.229] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.230] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.230] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.230] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.230] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.230] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.233] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.233] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.233] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.233] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:00.233] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:01.072] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:01.703] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.620] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.620] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.620] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.620] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.622] [puff::index::jointLog] [warning] Entry with header [miBART-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.622] [puff::index::jointLog] [warning] Entry with header [miBART-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-04 16:02:02.623] [puff::index::jointLog] [warning] Removed 789 transcripts that were sequence duplicates of indexed transcripts.
[2020-03-04 16:02:02.623] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-03-04 16:02:02.633] [puff::index::jointLog] [info] Replaced 110 non-ATCG nucleotides
[2020-03-04 16:02:02.633] [puff::index::jointLog] [info] Clipped poly-A tails from 1,524 transcripts
[2020-03-04 16:02:04.243] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-03-04 16:02:07.398] [puff::index::jointLog] [info] ntHll estimated 123752566 distinct k-mers, setting filter size to 2^31
[2020-03-04 16:39:17.912] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ref/GRCh38/Sequence/SalmonQuasiIndex/1.1.0/GencodeTranscriptome/25_1
[2020-03-04 16:39:18.684] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-03-04 16:39:19.006] [puff::index::jointLog] [info] contig count for validation: 1224219
[2020-03-04 16:39:19.895] [puff::index::jointLog] [info] Total # of Contigs : 1,224,219
[2020-03-04 16:39:19.895] [puff::index::jointLog] [info] Total # of numerical Contigs : 1,224,219
[2020-03-04 16:39:21.515] [puff::index::jointLog] [info] 
Total # of segments we have position for : 1,224,219
[2020-03-04 16:39:21.679] [puff::index::jointLog] [info] total contig vec entries 6,015,665
[2020-03-04 16:39:21.679] [puff::index::jointLog] [info] bits per offset entry 23
[2020-03-04 16:39:22.568] [puff::index::jointLog] [info] there were 779,113  equivalence classes
[2020-03-04 16:39:25.409] [puff::index::jointLog] [info] # segments = 1,224,219
[2020-03-04 16:39:25.409] [puff::index::jointLog] [info] total length = 161,576,681
[2020-03-04 16:39:25.501] [puff::index::jointLog] [error] Two references with the same name but different sequences: CDS_EBNA3B. We require that all input records have a unique name up to the first whitespace character.
[2020-03-05 08:06:06.588] [puff::index::jointLog] [info] Running fixFasta
[2020-03-05 08:06:08.897] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:09.004] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:09.542] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:10.480] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.069] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-05 08:06:12.142] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.330] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.330] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.330] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.564] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.565] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.566] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.566] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.566] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.566] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.566] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.568] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.568] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.568] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.568] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:12.568] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:13.415] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.020] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.942] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.942] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.942] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.942] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:06:14.943] [puff::index::jointLog] [error] In FixFasta, two references with the same name but different sequences: . We require that all input records have a unique name up to the first whitespace character.
[2020-03-05 08:18:37.225] [puff::index::jointLog] [info] Running fixFasta
[2020-03-05 08:18:39.403] [puff::index::jointLog] [warning] Entry with header [ENST00000473810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:39.525] [puff::index::jointLog] [warning] Entry with header [ENST00000603775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:39.933] [puff::index::jointLog] [warning] Entry with header [ENST00000637754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:40.873] [puff::index::jointLog] [warning] Entry with header [ENST00000632684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:42.649] [puff::index::jointLog] [warning] Entry with header [ENST00000626826] was longer than 200000 nucleotides.  This is probably a chromosome instead of a transcript.
[2020-03-05 08:18:42.728] [puff::index::jointLog] [warning] Entry with header [ENST00000543745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:42.936] [puff::index::jointLog] [warning] Entry with header [ENST00000415118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:42.936] [puff::index::jointLog] [warning] Entry with header [ENST00000434970], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:42.936] [puff::index::jointLog] [warning] Entry with header [ENST00000448914], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000439842], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390567], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000452198], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390569], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000437320], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390571], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390572], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000450276], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390574], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390575], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000431870], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390578], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000451044], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390580], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390581], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000431440], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390583], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390584], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390585], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000430425], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000454691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390588], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000414852], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390590], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.201] [puff::index::jointLog] [warning] Entry with header [ENST00000390591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.202] [puff::index::jointLog] [warning] Entry with header [ENST00000454908], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.202] [puff::index::jointLog] [warning] Entry with header [ENST00000518246], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.204] [puff::index::jointLog] [warning] Entry with header [ENST00000604642], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.204] [puff::index::jointLog] [warning] Entry with header [ENST00000603326], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.204] [puff::index::jointLog] [warning] Entry with header [ENST00000604950], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.204] [puff::index::jointLog] [warning] Entry with header [ENST00000603077], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.204] [puff::index::jointLog] [warning] Entry with header [ENST00000605284], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.207] [puff::index::jointLog] [warning] Entry with header [ENST00000604446], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.207] [puff::index::jointLog] [warning] Entry with header [ENST00000603693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.207] [puff::index::jointLog] [warning] Entry with header [ENST00000603935], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.207] [puff::index::jointLog] [warning] Entry with header [ENST00000604102], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:43.207] [puff::index::jointLog] [warning] Entry with header [ENST00000604838], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:44.125] [puff::index::jointLog] [warning] Entry with header [ENST00000579054], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:44.783] [puff::index::jointLog] [warning] Entry with header [ENST00000634174], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.798] [puff::index::jointLog] [warning] Entry with header [miBHFR1-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.798] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2*], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.798] [puff::index::jointLog] [warning] Entry with header [miBHFR1-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.798] [puff::index::jointLog] [warning] Entry with header [miBHFR1-3], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.800] [puff::index::jointLog] [warning] Entry with header [miBART-1], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.801] [puff::index::jointLog] [warning] Entry with header [miBART-2], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2020-03-05 08:18:45.801] [puff::index::jointLog] [warning] Removed 789 transcripts that were sequence duplicates of indexed transcripts.
[2020-03-05 08:18:45.801] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2020-03-05 08:18:45.810] [puff::index::jointLog] [info] Replaced 86 non-ATCG nucleotides
[2020-03-05 08:18:45.810] [puff::index::jointLog] [info] Clipped poly-A tails from 1,524 transcripts
[2020-03-05 08:18:47.482] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2020-03-05 08:18:50.206] [puff::index::jointLog] [info] ntHll estimated 123752566 distinct k-mers, setting filter size to 2^31
[2020-03-05 08:54:47.860] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ref/GRCh38/Sequence/SalmonQuasiIndex/1.1.0/GencodeTranscriptome/25_1
[2020-03-05 08:54:48.693] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2020-03-05 08:54:49.387] [puff::index::jointLog] [info] contig count for validation: 1224218
[2020-03-05 08:54:51.030] [puff::index::jointLog] [info] Total # of Contigs : 1,224,218
[2020-03-05 08:54:51.030] [puff::index::jointLog] [info] Total # of numerical Contigs : 1,224,218
[2020-03-05 08:54:54.895] [puff::index::jointLog] [info] 
Total # of segments we have position for : 1,224,218
[2020-03-05 08:54:55.098] [puff::index::jointLog] [info] total contig vec entries 6,015,664
[2020-03-05 08:54:55.098] [puff::index::jointLog] [info] bits per offset entry 23
[2020-03-05 08:54:56.984] [puff::index::jointLog] [info] there were 779,112  equivalence classes
[2020-03-05 08:55:04.520] [puff::index::jointLog] [info] # segments = 1,224,218
[2020-03-05 08:55:04.520] [puff::index::jointLog] [info] total length = 161,576,623
[2020-03-05 08:55:04.613] [puff::index::jointLog] [info] Reading the reference files ...
[2020-03-05 08:55:06.796] [puff::index::jointLog] [info] positional integer width = 28
[2020-03-05 08:55:06.797] [puff::index::jointLog] [info] seqSize = 161,576,623
[2020-03-05 08:55:06.797] [puff::index::jointLog] [info] rankSize = 161,576,623
[2020-03-05 08:55:06.797] [puff::index::jointLog] [info] edgeVecSize = 0
[2020-03-05 08:55:06.797] [puff::index::jointLog] [info] num keys = 124,850,083
[2020-03-05 08:55:40.038] [puff::index::jointLog] [info] mphf size = 77.9844 MB
[2020-03-05 08:55:40.038] [puff::index::jointLog] [info] chunk size = 80,788,312
[2020-03-05 08:55:40.038] [puff::index::jointLog] [info] chunk 0 = [0, 80,788,312)
[2020-03-05 08:55:40.038] [puff::index::jointLog] [info] chunk 1 = [80,788,312, 161,576,593)
[2020-03-05 08:56:13.342] [puff::index::jointLog] [info] finished populating pos vector
[2020-03-05 08:56:13.342] [puff::index::jointLog] [info] writing index components
[2020-03-05 08:56:15.963] [puff::index::jointLog] [info] finished writing dense pufferfish index