[2023-03-28 15:18:53.559] [puff::index::jointLog] [info] Running fixFasta
[2023-03-28 15:18:53.680] [puff::index::jointLog] [warning] Entry with header [rna35305], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.680] [puff::index::jointLog] [warning] Entry with header [rna35307], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.683] [puff::index::jointLog] [warning] Entry with header [rna35344], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.743] [puff::index::jointLog] [warning] Entry with header [rna35747], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.743] [puff::index::jointLog] [warning] Entry with header [rna35749], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.804] [puff::index::jointLog] [warning] Entry with header [rna36117], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.876] [puff::index::jointLog] [warning] Entry with header [rna40479], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.994] [puff::index::jointLog] [warning] Entry with header [rna41375], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.994] [puff::index::jointLog] [warning] Entry with header [rna41377], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.994] [puff::index::jointLog] [warning] Entry with header [rna41378], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:53.994] [puff::index::jointLog] [warning] Entry with header [rna41382], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.052] [puff::index::jointLog] [warning] Entry with header [rna41759], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.052] [puff::index::jointLog] [warning] Entry with header [rna41761], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.183] [puff::index::jointLog] [warning] Entry with header [rna28901], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.215] [puff::index::jointLog] [warning] Entry with header [rna29071], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.229] [puff::index::jointLog] [warning] Entry with header [rna29175], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.229] [puff::index::jointLog] [warning] Entry with header [rna29177], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.363] [puff::index::jointLog] [warning] Entry with header [rna29925], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.363] [puff::index::jointLog] [warning] Entry with header [rna29927], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.446] [puff::index::jointLog] [warning] Entry with header [rna30505], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.504] [puff::index::jointLog] [warning] Entry with header [rna30802], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.504] [puff::index::jointLog] [warning] Entry with header [rna30804], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.504] [puff::index::jointLog] [warning] Entry with header [rna30805], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.504] [puff::index::jointLog] [warning] Entry with header [rna30807], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.505] [puff::index::jointLog] [warning] Entry with header [rna30808], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.505] [puff::index::jointLog] [warning] Entry with header [rna30810], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.529] [puff::index::jointLog] [warning] Entry with header [rna17779], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.566] [puff::index::jointLog] [warning] Entry with header [rna18083], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.566] [puff::index::jointLog] [warning] Entry with header [rna18085], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18106], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18108], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18109], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18111], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18112], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.569] [puff::index::jointLog] [warning] Entry with header [rna18114], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.663] [puff::index::jointLog] [warning] Entry with header [rna18621], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.677] [puff::index::jointLog] [warning] Entry with header [rna18727], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.677] [puff::index::jointLog] [warning] Entry with header [rna18729], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.815] [puff::index::jointLog] [warning] Entry with header [rna19615], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.815] [puff::index::jointLog] [warning] Entry with header [rna19617], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.815] [puff::index::jointLog] [warning] Entry with header [rna19619], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.837] [puff::index::jointLog] [warning] Entry with header [rna19982], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.874] [puff::index::jointLog] [warning] Entry with header [rna20224], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.922] [puff::index::jointLog] [warning] Entry with header [rna20604], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.923] [puff::index::jointLog] [warning] Entry with header [rna20606], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.948] [puff::index::jointLog] [warning] Entry with header [rna20779], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.948] [puff::index::jointLog] [warning] Entry with header [rna20781], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:54.991] [puff::index::jointLog] [warning] Entry with header [rna33087], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.116] [puff::index::jointLog] [warning] Entry with header [rna33916], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.116] [puff::index::jointLog] [warning] Entry with header [rna33918], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.221] [puff::index::jointLog] [warning] Entry with header [rna34387], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.387] [puff::index::jointLog] [warning] Entry with header [rna24300], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.411] [puff::index::jointLog] [warning] Entry with header [rna24485], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.411] [puff::index::jointLog] [warning] Entry with header [rna24487], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.411] [puff::index::jointLog] [warning] Entry with header [rna24488], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.439] [puff::index::jointLog] [warning] Entry with header [rna24665], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.532] [puff::index::jointLog] [warning] Entry with header [rna25229], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.532] [puff::index::jointLog] [warning] Entry with header [rna25231], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.562] [puff::index::jointLog] [warning] Entry with header [rna25516], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.562] [puff::index::jointLog] [warning] Entry with header [rna25518], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.771] [puff::index::jointLog] [warning] Entry with header [rna47419], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.771] [puff::index::jointLog] [warning] Entry with header [rna47421], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.905] [puff::index::jointLog] [warning] Entry with header [rna48331], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.905] [puff::index::jointLog] [warning] Entry with header [rna48333], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:55.937] [puff::index::jointLog] [warning] Entry with header [rna26285], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.032] [puff::index::jointLog] [warning] Entry with header [rna26691], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.032] [puff::index::jointLog] [warning] Entry with header [rna26693], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.165] [puff::index::jointLog] [warning] Entry with header [rna27789], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.165] [puff::index::jointLog] [warning] Entry with header [rna27791], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.516] [puff::index::jointLog] [warning] Entry with header [rna32000], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.516] [puff::index::jointLog] [warning] Entry with header [rna32002], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.550] [puff::index::jointLog] [warning] Entry with header [rna32250], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.550] [puff::index::jointLog] [warning] Entry with header [rna32252], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.550] [puff::index::jointLog] [warning] Entry with header [rna32254], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.583] [puff::index::jointLog] [warning] Entry with header [rna32511], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.583] [puff::index::jointLog] [warning] Entry with header [rna32513], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.583] [puff::index::jointLog] [warning] Entry with header [rna32514], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.583] [puff::index::jointLog] [warning] Entry with header [rna32516], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.583] [puff::index::jointLog] [warning] Entry with header [rna32517], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.709] [puff::index::jointLog] [warning] Entry with header [rna21435], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.709] [puff::index::jointLog] [warning] Entry with header [rna21437], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.734] [puff::index::jointLog] [warning] Entry with header [rna21591], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.734] [puff::index::jointLog] [warning] Entry with header [rna21593], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.891] [puff::index::jointLog] [warning] Entry with header [rna22659], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.891] [puff::index::jointLog] [warning] Entry with header [rna22661], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.891] [puff::index::jointLog] [warning] Entry with header [rna22663], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.891] [puff::index::jointLog] [warning] Entry with header [rna22664], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.891] [puff::index::jointLog] [warning] Entry with header [rna22666], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:56.902] [puff::index::jointLog] [warning] Entry with header [rna22754], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.054] [puff::index::jointLog] [warning] Entry with header [TCONS_00081670], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.125] [puff::index::jointLog] [warning] Entry with header [rna6378], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.125] [puff::index::jointLog] [warning] Entry with header [rna6380], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.128] [puff::index::jointLog] [warning] Entry with header [rna6392], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.264] [puff::index::jointLog] [warning] Entry with header [ENSDART00000182373], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.264] [puff::index::jointLog] [warning] Entry with header [ENSDART00000193530], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.264] [puff::index::jointLog] [warning] Entry with header [ENSDART00000184666], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.264] [puff::index::jointLog] [warning] Entry with header [ENSDART00000181734], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.265] [puff::index::jointLog] [warning] Entry with header [ENSDART00000183389], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.265] [puff::index::jointLog] [warning] Entry with header [ENSDART00000187118], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.285] [puff::index::jointLog] [warning] Entry with header [rna7098], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.285] [puff::index::jointLog] [warning] Entry with header [rna7100], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.285] [puff::index::jointLog] [warning] Entry with header [rna7101], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.334] [puff::index::jointLog] [warning] Entry with header [rna7615], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.334] [puff::index::jointLog] [warning] Entry with header [rna7617], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.469] [puff::index::jointLog] [warning] Entry with header [rna57676], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.481] [puff::index::jointLog] [warning] Entry with header [TCONS_00070140], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.562] [puff::index::jointLog] [warning] Entry with header [rna58298], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.569] [puff::index::jointLog] [warning] Entry with header [rna58348], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.569] [puff::index::jointLog] [warning] Entry with header [rna58351], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.569] [puff::index::jointLog] [warning] Entry with header [rna58354], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.569] [puff::index::jointLog] [warning] Entry with header [rna58356], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.569] [puff::index::jointLog] [warning] Entry with header [rna58358], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.613] [puff::index::jointLog] [warning] Entry with header [rna58611], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.613] [puff::index::jointLog] [warning] Entry with header [rna58613], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.655] [puff::index::jointLog] [warning] Entry with header [rna58951], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.659] [puff::index::jointLog] [warning] Entry with header [rna58984], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.820] [puff::index::jointLog] [warning] Entry with header [rna56222], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.846] [puff::index::jointLog] [warning] Entry with header [TCONS_00068598], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.857] [puff::index::jointLog] [warning] Entry with header [rna56485], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.920] [puff::index::jointLog] [warning] Entry with header [rna57072], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.920] [puff::index::jointLog] [warning] Entry with header [rna57074], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.920] [puff::index::jointLog] [warning] Entry with header [rna57076], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.998] [puff::index::jointLog] [warning] Entry with header [rna50740], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:57.998] [puff::index::jointLog] [warning] Entry with header [rna50742], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.047] [puff::index::jointLog] [warning] Entry with header [rna51157], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.047] [puff::index::jointLog] [warning] Entry with header [rna51158], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.047] [puff::index::jointLog] [warning] Entry with header [rna51160], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.228] [puff::index::jointLog] [warning] Entry with header [rna52597], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.442] [puff::index::jointLog] [warning] Entry with header [rna62267], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.449] [puff::index::jointLog] [warning] Entry with header [rna62317], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.449] [puff::index::jointLog] [warning] Entry with header [rna62319], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.486] [puff::index::jointLog] [warning] Entry with header [rna75], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.614] [puff::index::jointLog] [warning] Entry with header [rna944], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.646] [puff::index::jointLog] [warning] Entry with header [rna1168], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.657] [puff::index::jointLog] [warning] Entry with header [rna1256], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.729] [puff::index::jointLog] [warning] Entry with header [rna1744], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.729] [puff::index::jointLog] [warning] Entry with header [rna1746], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.729] [puff::index::jointLog] [warning] Entry with header [rna1748], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.791] [puff::index::jointLog] [warning] Entry with header [rna2223], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.822] [puff::index::jointLog] [warning] Entry with header [rna38703], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.822] [puff::index::jointLog] [warning] Entry with header [rna38705], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.822] [puff::index::jointLog] [warning] Entry with header [rna38707], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.822] [puff::index::jointLog] [warning] Entry with header [rna38709], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.938] [puff::index::jointLog] [warning] Entry with header [rna39515], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:58.938] [puff::index::jointLog] [warning] Entry with header [rna39517], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.098] [puff::index::jointLog] [warning] Entry with header [rna40029], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.098] [puff::index::jointLog] [warning] Entry with header [rna40031], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.200] [puff::index::jointLog] [warning] Entry with header [rna59689], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.278] [puff::index::jointLog] [warning] Entry with header [rna60217], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.278] [puff::index::jointLog] [warning] Entry with header [rna60219], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.278] [puff::index::jointLog] [warning] Entry with header [rna60220], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.340] [puff::index::jointLog] [warning] Entry with header [rna60684], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.340] [puff::index::jointLog] [warning] Entry with header [rna60686], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.383] [puff::index::jointLog] [warning] Entry with header [rna2667], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.383] [puff::index::jointLog] [warning] Entry with header [rna2669], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.391] [puff::index::jointLog] [warning] Entry with header [rna2746], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.391] [puff::index::jointLog] [warning] Entry with header [rna2748], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.391] [puff::index::jointLog] [warning] Entry with header [rna2749], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.408] [puff::index::jointLog] [warning] Entry with header [ENSDART00000192604], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.479] [puff::index::jointLog] [warning] Entry with header [rna3428], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.479] [puff::index::jointLog] [warning] Entry with header [rna3430], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.500] [puff::index::jointLog] [warning] Entry with header [rna3579], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.579] [puff::index::jointLog] [warning] Entry with header [TCONS_00051188], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.694] [puff::index::jointLog] [warning] Entry with header [rna4978], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.694] [puff::index::jointLog] [warning] Entry with header [rna4980], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.708] [puff::index::jointLog] [warning] Entry with header [rna5088], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.708] [puff::index::jointLog] [warning] Entry with header [rna5090], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.863] [puff::index::jointLog] [warning] Entry with header [rna37743], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.863] [puff::index::jointLog] [warning] Entry with header [rna37745], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.863] [puff::index::jointLog] [warning] Entry with header [rna37746], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:18:59.863] [puff::index::jointLog] [warning] Entry with header [rna37748], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.084] [puff::index::jointLog] [warning] Entry with header [rna43034], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.101] [puff::index::jointLog] [warning] Entry with header [rna43125], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.113] [puff::index::jointLog] [warning] Entry with header [rna43213], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.144] [puff::index::jointLog] [warning] Entry with header [rna43466], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.144] [puff::index::jointLog] [warning] Entry with header [rna43468], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.292] [puff::index::jointLog] [warning] Entry with header [rna44624], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.413] [puff::index::jointLog] [warning] Entry with header [rna9100], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.491] [puff::index::jointLog] [warning] Entry with header [rna9721], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.531] [puff::index::jointLog] [warning] Entry with header [TCONS_00089029], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.682] [puff::index::jointLog] [warning] Entry with header [rna16940], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.826] [puff::index::jointLog] [warning] Entry with header [rna49056], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.843] [puff::index::jointLog] [warning] Entry with header [ENSDART00000183775], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.881] [puff::index::jointLog] [warning] Entry with header [rna49448], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.881] [puff::index::jointLog] [warning] Entry with header [rna49450], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.943] [puff::index::jointLog] [warning] Entry with header [rna49795], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:00.954] [puff::index::jointLog] [warning] Entry with header [ENSDART00000186673], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.018] [puff::index::jointLog] [warning] Entry with header [rna50149], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.039] [puff::index::jointLog] [warning] Entry with header [rna50306], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.127] [puff::index::jointLog] [warning] Entry with header [TCONS_00037038], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.180] [puff::index::jointLog] [warning] Entry with header [rna45502], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.180] [puff::index::jointLog] [warning] Entry with header [rna45504], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.199] [puff::index::jointLog] [warning] Entry with header [rna45656], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.202] [puff::index::jointLog] [warning] Entry with header [rna45710], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.303] [puff::index::jointLog] [warning] Entry with header [rna46346], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.303] [puff::index::jointLog] [warning] Entry with header [rna46348], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.415] [puff::index::jointLog] [warning] Entry with header [rna53226], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:01.796] [puff::index::jointLog] [warning] Entry with header [rna55177], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:02.142] [puff::index::jointLog] [warning] Entry with header [rna63173], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-03-28 15:19:24.610] [puff::index::jointLog] [warning] Removed 92 transcripts that were sequence duplicates of indexed transcripts.
[2023-03-28 15:19:24.610] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2023-03-28 15:19:24.615] [puff::index::jointLog] [info] Replaced 4713671 non-ATCG nucleotides
[2023-03-28 15:19:24.615] [puff::index::jointLog] [info] Clipped poly-A tails from 635 transcripts
[2023-03-28 15:19:27.087] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2023-03-28 15:19:39.317] [puff::index::jointLog] [info] ntHll estimated 1077673173 distinct k-mers, setting filter size to 2^35
[2023-03-28 16:35:20.300] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2023-03-28 16:35:20.300] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory SalmonIndex
[2023-03-28 16:35:24.197] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2023-03-28 16:35:24.710] [puff::index::jointLog] [info] contig count for validation: 25131862
[2023-03-28 16:35:38.481] [puff::index::jointLog] [info] Total # of Contigs : 25131862
[2023-03-28 16:35:38.481] [puff::index::jointLog] [info] Total # of numerical Contigs : 25131862
[2023-03-28 16:35:39.541] [puff::index::jointLog] [info] Total # of contig vec entries: 225582598
[2023-03-28 16:35:39.541] [puff::index::jointLog] [info] bits per offset entry 28
[2023-03-28 16:35:45.621] [puff::index::jointLog] [info] Done constructing the contig vector. 25131863
[2023-03-28 16:36:02.121] [puff::index::jointLog] [info] # segments = 25131862
[2023-03-28 16:36:02.121] [puff::index::jointLog] [info] total length = 1838420121
[2023-03-28 16:36:02.238] [puff::index::jointLog] [info] Reading the reference files ...
[2023-03-28 16:36:09.088] [puff::index::jointLog] [info] positional integer width = 31
[2023-03-28 16:36:09.088] [puff::index::jointLog] [info] seqSize = 1838420121
[2023-03-28 16:36:09.088] [puff::index::jointLog] [info] rankSize = 1838420121
[2023-03-28 16:36:09.088] [puff::index::jointLog] [info] edgeVecSize = 0
[2023-03-28 16:36:09.088] [puff::index::jointLog] [info] num keys = 1084464261
[2023-03-28 16:39:42.881] [puff::index::jointLog] [info] mphf size = 677.413 MB
[2023-03-28 16:39:43.754] [puff::index::jointLog] [info] chunk size = 1838420121
[2023-03-28 16:39:43.756] [puff::index::jointLog] [info] chunk 0 = [0, 1838420091)
[2023-03-28 16:44:13.579] [puff::index::jointLog] [info] finished populating pos vector
[2023-03-28 16:44:13.579] [puff::index::jointLog] [info] writing index components
[2023-03-28 16:44:21.155] [puff::index::jointLog] [info] finished writing dense pufferfish index