thomaskf
commented
2 years ago Hi, Thanks for your comment. Which version of IQ-Tree are you running? Can you also send us the .log file? Under which platform did IQ-Tree run? Thanks! Thomas
Closed Wenwen012345 closed 2 years ago
thomaskf
commented
2 years ago Hi, Thanks for your comment. Which version of IQ-Tree are you running? Can you also send us the .log file? Under which platform did IQ-Tree run? Thanks! Thomas
Wenwen012345
commented
2 years ago Hi, @thomaskf Thanks for your reply. Actually I have tried 2.1.2, 2.1.4-beta and 2.2.0-beta three versions. In both versions 2.1.4-beta and 2.0-beta, there was a "Creating fast initial parsimony tree by random order stepwise addition..." stoped phenomenon, meaning no further steps were taken. This process remained unchanged for more than a dozen hours. It's worth noting that I use Linux Ubuntu, but I can't install the latest version of IQ-Tree and its MaffT (sequence matching software) under the default Conda environment. Display errors are HTTP-like errors. However, I can install the latest version of IQ-Tree and Mafft when I create a new environment. But as I said, it's stuck somewhere. I don't know why.
But the last time I tried version 2.1.2, I should be able to run the full process, still running. But version 2.1.2 is too old. My command line is: iqtree2 -s ty3.mafft -v -T AUTO -bb 1000 -nt AUTO -m Q.mammal+F+G4
Logfile is displayed as follows:
IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: ubuntu-server (AVX512, FMA3, 125 GB RAM) Command: iqtree2 -s ty3.mafft -v -T AUTO -bb 1000 -nt AUTO -m Q.mammal+F+G4 Seed: 862280 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sun Apr 24 15:29:23 2022 Kernel: AVX+FMA - auto-detect threads (40 CPU cores detected)
Reading alignment file ty3.mafft ... Fasta format detected Name shortening took 0.012561 seconds. Duplicate sequence name check took 0.008828 seconds. Alignment most likely contains protein sequences Alignment has 7506 sequences with 451 columns, 439 distinct patterns 231 parsimony-informative, 112 singleton sites, 108 constant sites WARNING: Some sequence names are changed as follows: 2_CM030788.1:10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT -> 2_CM030788.1_1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 2_CM030788.1:16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT ....
Empirical state frequencies: 0.0614272274 0.0566535631 0.0387584577 0.0627073119 0.0257267529 0.0301913255 0.0464098194 0.0631023050 0.0274071993 0.0523546575 0.0898490910 0.0752121036 0.0341972460 0.0647436356 0.0459189542 0.0434140076 0.0497822169 0.0133569492 0.0442737887 0.0745133876 Gap/Ambiguity Composition p-value 1 2_CM030788.1_10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 77.83% passed 98.73% 2 2_CM030788.1_10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 97.05% 3 2_CM030788.1_11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.31% passed 99.48% 4 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 99.51% 5 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 89.30% 6 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.82% 7 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 93.97% 8 2_CM030788.1_13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 96.08% 9 2_CM030788.1_13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.21% 10 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 93.20% 11 2_CM030788.1_13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.64% 12 2_CM030788.1_13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 85.10% 13 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.85% 14 2_CM030788.1_14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 63.41% passed 84.90% 15 2_CM030788.1_14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 84.87% 16 2_CM030788.1_14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.25% 17 2_CM030788.1_14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.15% 18 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 93.97% 19 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 20 2_CM030788.1_15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 78.51% 21 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.85% 22 2_CM030788.1_16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 92.96% 23 2_CM030788.1_1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.64% passed 74.53% 24 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.30% 25 2_CM030788.1_17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.51% 26 2_CM030788.1_17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.81% 27 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 98.51% 28 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.99% 29 2_CM030788.1_18029260..18040301|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.08% passed 98.02% 30 2_CM030788.1_18097061..18108009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.58% 31 2_CM030788.1_18226675..18235295|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 32 2_CM030788.1_18436793..18449962|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.16% 33 2_CM030788.1_18452338..18464451|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.84% 34 2_CM030788.1_18837081..18852233|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.75% 35 2_CM030788.1_19294810..19305171|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.51% passed 98.46% 36 2_CM030788.1_19491541..19503155|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.86% 37 2_CM030788.1_19524791..19538180|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 96.77% 38 2_CM030788.1_19548749..19555834|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.64% passed 66.16% 39 2_CM030788.1_19788203..19799256|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 83.98% 40 2_CM030788.1_19901534..19915196|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.28% passed 89.07% 41 2_CM030788.1_19928699..19940745|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.80% 42 2_CM030788.1_20101941..20107197|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.86% passed 91.60% 43 2_CM030788.1_20187873..20196495|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 87.89% 44 2_CM030788.1_20377621..20392414|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.64% passed 99.20% 45 2_CM030788.1_20869356..20877883|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.41% 46 2_CM030788.1_20939586..20950906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 99.95% 47 2_CM030788.1_2126144..2136464|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 99.41% 48 2_CM030788.1_21334938..21344524|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 62.31% passed 97.02% 49 2_CM030788.1_21420590..21429130|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.41% 50 2_CM030788.1_21442406..21453235|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.86% 51 2_CM030788.1_21462891..21474123|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.27% 52 2_CM030788.1_21480152..21491691|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.06% 53 2_CM030788.1_21667170..21675797|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 54 2_CM030788.1_21788631..21802124|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 63.74% 55 2_CM030788.1_21807446..21820649|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 73.61% passed 67.55% 56 2_CM030788.1_21842687..21852156|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 80.04% passed 15.34% 57 2_CM030788.1_21939314..21950563|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.92% 58 2_CM030788.1_2214666..2226279|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.63% 59 2_CM030788.1_22541547..22552941|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.98% 60 2_CM030788.1_22567605..22579550|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.83% 61 2_CM030788.1_22694941..22703598|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.23% 62 2_CM030788.1_22998464..23012098|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.96% 63 2_CM030788.1_23151442..23166164|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 97.45% 64 2_CM030788.1_23254039..23262578|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 92.79% 65 2_CM030788.1_23269034..23280792|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 71.40% passed 65.73% 66 2_CM030788.1_23689926..23701352|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 87.66% 67 2_CM030788.1_23738222..23754887|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 97.47% 68 2_CM030788.1_24109198..24121901|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 67.18% passed 86.42% 69 2_CM030788.1_24249343..24260618|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.78% 70 2_CM030788.1_24352697..24367856|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.55% 71 2_CM030788.1_24378864..24390260|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.53% passed 88.03% 72 2_CM030788.1_24414443..24426426|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 79.98% 73 2_CM030788.1_24487360..24499939|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.71% 74 2_CM030788.1_24521764..24534048|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.64% passed 92.90% 75 2_CM030788.1_24778905..24791320|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.91% 76 2_CM030788.1_24871492..24885019|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 98.97% 77 2_CM030788.1_25128439..25139904|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.27% 78 2_CM030788.1_25375446..25387125|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 73.17% passed 84.83% 79 2_CM030788.1_25797881..25809278|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.67% 80 2_CM030788.1_25976816..25985452|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.86% passed 90.19% 81 2_CM030788.1_26010490..26021517|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.78% 82 2_CM030788.1_26304347..26312971|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 91.47% 83 2_CM030788.1_26658817..26670192|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 94.64% 84 2_CM030788.1_26791286..26802720|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.51% passed 10.31% 85 2_CM030788.1_26805654..26814510|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 97.80% 86 2_CM030788.1_26967092..26979598|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.75% 87 2_CM030788.1_27076828..27092326|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.71% 88 2_CM030788.1_27125707..27140558|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.26% 89 2_CM030788.1_27304250..27318389|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 99.46% 90 2_CM030788.1_28023425..28034575|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.96% 91 2_CM030788.1_28345270..28358043|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.86% 92 2_CM030788.1_2836517..2849514|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 64.97% passed 97.04% 93 2_CM030788.1_28407035..28419116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.95%
... WARNING: 7506 sequences contain more than 50% gaps/ambiguity **** TOTAL 62.37% 7 sequences failed composition chi2 test (p-value<5%; df=19) Hashing sequences took 0.050 wall-clock seconds NOTE: 2_CM030791.1_43627819..43638172|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_392134..400756|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_59366905..59378629|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_25018583..25032128|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_9260856..9272415|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_18226675..18235295|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_39278378..39290782|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_8930128..8940872|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_36086242..36099596|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_2756267..2767813|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_38786434..38795065|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_20187873..20196495|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_2875475..2883998|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_20869356..20877883|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_18067260..18077646|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_2126144..2136464|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_24824355..24837835|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_21788631..21802124|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_24225600..24234256|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_22694941..22703598|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_34889596..34904094|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_26967092..26979598|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_56633949..56645542|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_2990121..3001728|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030794.1_51510846..51522557|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_31209378..31219311|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_39043989..39055702|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_33282147..33293906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10502418..10513681|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_36875300..36886645|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036312.1_23834180..23846196|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_42043157..42056631|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_9101272..9112687|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_4545353..4557009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_36703494..36715457|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_4693758..4706916|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_27741471..27750564|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_479008..488088|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_50979921..50992328|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_49284537..49296937|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_28837980..28850097|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_49317467..49327011|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_58211569..58225040|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_51506455..51519906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10267893..10281008|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_52297442..52310708|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10204007..10212623|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_53084986..53093615|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_17130032..17141071|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_54623561..54636260|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_56660120..56668987|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_59379762..59388660|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030796.1_11845407..11857664|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_630225..642500|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_51699695..51712183|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_8100639..8113474|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_25448344..25460367|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_8927360..8939322|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_31653244..31664936|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_9423355..9437417|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_33084819..33090459|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030788.1_9959744..9965388|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_42270484..42279117|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_10869411..10878035|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_7801283..7811632|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_10888133..10901446|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis
...
Alignment was printed to ty3.mafft.uniqueseq.phy
For your convenience alignment with unique sequences printed to ty3.mafft.uniqueseq.phy Empirical state frequencies: 0.0609755283 0.0565089695 0.0385732441 0.0627584945 0.0256636547 0.0303021098 0.0462902874 0.0627191778 0.0274731368 0.0523020836 0.0900259904 0.0755611059 0.0343947029 0.0647983906 0.0457563119 0.0436825851 0.0499330245 0.0134233633 0.0444040007 0.0744538382 Creating fast initial parsimony tree by random order stepwise addition...
It stops at that point.
Please answer for me, thank you!
Wenwen012345
commented
2 years ago Latest news, IQ-Tree seems to be working again, I really don't know why. It seems that a program that someone else ran during the previous run took up my run resources and was stuck there. Anyway thank you!!
Wenwen012345
commented
2 years ago HELLO again, @thomaskf A new problem has arisen. There was a power cut last night, so I hadn't noticed it before. As mentioned above, the tree building process stops again. What I constructed was a family tree of LTR retrotransposons. Divided into TY1 family and TY3 family. In previous tests, the TY1 family has been able to carry out the tree process normally. But the tree flow of TY3 is stuck in the middle ('Creating fast initial parsimony tree by random order stepwise addition...') as mentioned above. I don't know if this is reason: the two tree builds are done together. But it takes a long time to build a single tree, more than 24 hours, 2,000 sequences. And if I don't do it together it's going to take a lot of time. Could you give me some advice?
thomaskf
commented
2 years ago Hi Wensulin93, Can you try version 2.2.0.2? We have fixed a few issues in this version. From your previous log file, the version was 2.1.4. If the same thing happens for version 2.2.0.2, can you send us the log file too? Thank you.
Wenwen012345
commented
2 years ago IQ-TREE multicore version 2.2.0-beta COVID-edition for Linux 64-bit built Mar 3 2022 built Mar 3 2022 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.
Host: ubuntu-server (AVX512, FMA3, 125 GB RAM) Command: iqtree2 -s ty3.mafft -v -bb 1000 -nt AUTO -m Q.mammal+F+G4 Seed: 124272 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Thu Apr 28 08:40:06 2022 Kernel: AVX+FMA - auto-detect threads (40 CPU cores detected)
Reading alignment file ty3.mafft ... Fasta format detected Reading fasta file: done in 2.22957 secs using 4.627% CPU Name shortening took 0.021048 seconds. Duplicate sequence name check took 0.023836 seconds. Sequence Type detection took 0.062675 seconds. Alignment most likely contains protein sequences Constructing alignment: done in 0.161021 secs using 485.9% CPU Time to read input file was 2.927941 sec. Time to count constant sites was 0.000008 sec. Alignment has 7506 sequences with 451 columns, 439 distinct patterns 231 parsimony-informative, 112 singleton sites, 108 constant sites WARNING: Some sequence names are changed as follows: 2_CM030788.1:10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RT -> 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 2_CM030788.1:16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT -> 2_CM030788.1_16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 2_CM030788.1:1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT -> 2_CM030788.1_1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 2_CM030788.1:16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre:Ty3-RT -> 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 2_CM030788.1:1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:18029260..18040301|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> 2_CM030788.1_18029260..18040301|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 2_CM030788.1:18097061..18108009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand:Ty3-RT -> ...
Alignment state count time was 0.018981 seconds. Empirical state frequencies: 0.0614272274 0.0566535631 0.0387584577 0.0627073119 0.0257267529 0.0301913255 0.0464098194 0.0631023050 0.0274071993 0.0523546575 0.0898490910 0.0752121036 0.0341972460 0.0647436356 0.0459189542 0.0434140076 0.0497822169 0.0133569492 0.0442737887 0.0745133876 Gap/Ambiguity Composition p-value Analyzing sequences: done in 0.0479822 secs using 1651% CPU 1 2_CM030788.1_10112084..10123425|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 77.83% passed 98.73% 2 2_CM030788.1_10509838..10522103|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 97.05% 3 2_CM030788.1_11284690..11296229|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.31% passed 99.48% 4 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 99.51% 5 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 89.30% 6 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.82% 7 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 93.97% 8 2_CM030788.1_13104171..13115584|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 96.08% 9 2_CM030788.1_13386404..13402038|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.21% 10 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 93.20% 11 2_CM030788.1_13626038..13637480|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.64% 12 2_CM030788.1_13724942..13736133|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 85.10% 13 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.85% 14 2_CM030788.1_14737732..14752625|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 63.41% passed 84.90% 15 2_CM030788.1_14779615..14792701|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 84.87% 16 2_CM030788.1_14873187..14883309|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.25% 17 2_CM030788.1_14912400..14924444|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.15% 18 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 93.97% 19 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 20 2_CM030788.1_15162263..15170871|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 78.51% 21 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.85% 22 2_CM030788.1_16329010..16337866|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 92.96% 23 2_CM030788.1_1683177..1688833|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.64% passed 74.53% 24 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.30% 25 2_CM030788.1_17061848..17072217|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.51% 26 2_CM030788.1_17222228..17234790|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.81% 27 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 98.51% 28 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.99% 29 2_CM030788.1_18029260..18040301|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.08% passed 98.02% 30 2_CM030788.1_18097061..18108009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.58% 31 2_CM030788.1_18226675..18235295|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 32 2_CM030788.1_18436793..18449962|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.16% 33 2_CM030788.1_18452338..18464451|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.84% 34 2_CM030788.1_18837081..18852233|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.75% 35 2_CM030788.1_19294810..19305171|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.51% passed 98.46% 36 2_CM030788.1_19491541..19503155|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.86% 37 2_CM030788.1_19524791..19538180|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 96.77% 38 2_CM030788.1_19548749..19555834|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.64% passed 66.16% 39 2_CM030788.1_19788203..19799256|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 83.98% 40 2_CM030788.1_19901534..19915196|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.28% passed 89.07% 41 2_CM030788.1_19928699..19940745|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.80% 42 2_CM030788.1_20101941..20107197|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT 61.86% passed 91.60% 43 2_CM030788.1_20187873..20196495|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 87.89% 44 2_CM030788.1_20377621..20392414|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.64% passed 99.20% 45 2_CM030788.1_20869356..20877883|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.41% 46 2_CM030788.1_20939586..20950906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 99.95% 47 2_CM030788.1_2126144..2136464|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 99.41% 48 2_CM030788.1_21334938..21344524|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 62.31% passed 97.02% 49 2_CM030788.1_21420590..21429130|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.41% 50 2_CM030788.1_21442406..21453235|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.86% 51 2_CM030788.1_21462891..21474123|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.27% 52 2_CM030788.1_21480152..21491691|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.06% 53 2_CM030788.1_21667170..21675797|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 84.97% 54 2_CM030788.1_21788631..21802124|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 60.98% passed 63.74% 55 2_CM030788.1_21807446..21820649|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 73.61% passed 67.55% 56 2_CM030788.1_21842687..21852156|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 80.04% passed 15.34% 57 2_CM030788.1_21939314..21950563|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.92% 58 2_CM030788.1_2214666..2226279|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.63% 59 2_CM030788.1_22541547..22552941|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.98% 60 2_CM030788.1_22567605..22579550|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.83% 61 2_CM030788.1_22694941..22703598|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 94.23% 62 2_CM030788.1_22998464..23012098|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.96% 63 2_CM030788.1_23151442..23166164|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 97.45% 64 2_CM030788.1_23254039..23262578|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 92.79% 65 2_CM030788.1_23269034..23280792|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 71.40% passed 65.73% 66 2_CM030788.1_23689926..23701352|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 87.66% 67 2_CM030788.1_23738222..23754887|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 97.47% 68 2_CM030788.1_24109198..24121901|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 67.18% passed 86.42% 69 2_CM030788.1_24249343..24260618|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.78% 70 2_CM030788.1_24352697..24367856|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.55% 71 2_CM030788.1_24378864..24390260|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 62.53% passed 88.03% 72 2_CM030788.1_24414443..24426426|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 79.98% 73 2_CM030788.1_24487360..24499939|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.71% 74 2_CM030788.1_24521764..24534048|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.64% passed 92.90% 75 2_CM030788.1_24778905..24791320|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.91% 76 2_CM030788.1_24871492..24885019|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 98.97% 77 2_CM030788.1_25128439..25139904|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.27% 78 2_CM030788.1_25375446..25387125|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 73.17% passed 84.83% 79 2_CM030788.1_25797881..25809278|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.67% 80 2_CM030788.1_25976816..25985452|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.86% passed 90.19% 81 2_CM030788.1_26010490..26021517|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.78% 82 2_CM030788.1_26304347..26312971|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 91.47% 83 2_CM030788.1_26658817..26670192|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 94.64% 84 2_CM030788.1_26791286..26802720|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 72.51% passed 10.31% 85 2_CM030788.1_26805654..26814510|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 97.80% 86 2_CM030788.1_26967092..26979598|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.75% 87 2_CM030788.1_27076828..27092326|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.71% 88 2_CM030788.1_27125707..27140558|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.26% 89 2_CM030788.1_27304250..27318389|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 99.46% 90 2_CM030788.1_28023425..28034575|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.96% 91 2_CM030788.1_28345270..28358043|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.86% 92 2_CM030788.1_2836517..2849514|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 64.97% passed 97.04% 93 2_CM030788.1_28407035..28419116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.95% 94 2_CM030788.1_28831218..28843788|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.72% 95 2_CM030788.1_28942889..28954942|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 95.77% 96 2_CM030788.1_29232745..29244007|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.98% 97 2_CM030788.1_29246754..29261853|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 99.59% 98 2_CM030788.1_2925494..2936986|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.73% 99 2_CM030788.1_29354581..29366848|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.94% 100 2_CM030788.1_29855224..29866869|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.61% 101 2_CM030788.1_2990121..3001728|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.99% 102 2_CM030788.1_29976721..29989508|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.64% passed 97.09% 103 2_CM030788.1_30042966..30054417|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 78.49% passed 90.10% 104 2_CM030788.1_30256997..30268375|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 65.85% passed 99.10% 105 2_CM030788.1_30430785..30442552|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.21% 106 2_CM030788.1_30822450..30834692|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.19% 107 2_CM030788.1_30896096..30906841|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.96% 108 2_CM030788.1_31209378..31219311|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 96.72% 109 2_CM030788.1_31636311..31647266|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.72% 110 2_CM030788.1_31803207..31815575|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 97.84% 111 2_CM030788.1_31892824..31904542|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 94.23% 112 2_CM030788.1_31999436..32010771|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 97.55% 113 2_CM030788.1_32017168..32028021|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.83% 114 2_CM030788.1_32628678..32637261|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 65.85% passed 76.58% 115 2_CM030788.1_32856496..32868236|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.42% 116 2_CM030788.1_32900676..32914189|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 93.34% 117 2_CM030788.1_33148058..33161792|unknown|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.61% 118 2_CM030788.1_33282147..33293906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.37% 119 2_CM030788.1_33321671..33333691|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 76.05% passed 94.97% 120 2_CM030788.1_33367296..33379070|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 96.27% 121 2_CM030788.1_33571367..33583660|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 97.92% 122 2_CM030788.1_34095336..34108513|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 73.39% passed 74.74% 123 2_CM030788.1_34812510..34823620|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.93% 124 2_CM030788.1_34830385..34842722|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.42% 125 2_CM030788.1_34889596..34904094|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.75% 126 2_CM030788.1_35361859..35376326|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.24% 127 2_CM030788.1_35520447..35533938|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 89.59% 128 2_CM030788.1_36633638..36645387|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 94.10% 129 2_CM030788.1_36875300..36886645|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.92% 130 2_CM030788.1_36984665..36997922|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 65.19% passed 98.80% 131 2_CM030788.1_37837924..37849868|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 99.83% 132 2_CM030788.1_37964252..37975268|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.92% 133 2_CM030788.1_38057935..38069352|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 97.65% 134 2_CM030788.1_38112484..38123957|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 98.31% 135 2_CM030788.1_38366352..38377813|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 80.27% passed 92.13% 136 2_CM030788.1_38786434..38795065|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 87.89% 137 2_CM030788.1_38827809..38839436|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 85.23% 138 2_CM030788.1_38871823..38883260|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.72% 139 2_CM030788.1_38909023..38921483|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 87.36% passed 39.45% 140 2_CM030788.1_39021963..39032989|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.68% 141 2_CM030788.1_39043989..39055702|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.37% 142 2_CM030788.1_39118046..39126692|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 63.40% 143 2_CM030788.1_39188288..39200822|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.54% 144 2_CM030788.1_39364959..39376197|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.86% passed 99.99% 145 2_CM030788.1_39576112..39587028|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.88% 146 2_CM030788.1_39856066..39863624|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 88.73% 147 2_CM030788.1_39974857..39986953|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.80% 148 2_CM030788.1_40023041..40035063|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.82% 149 2_CM030788.1_40050910..40060934|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 98.35% 150 2_CM030788.1_40105225..40118006|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.86% 151 2_CM030788.1_40535230..40546326|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 76.94% passed 96.31% 152 2_CM030788.1_40564554..40575255|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.71% 153 2_CM030788.1_40784426..40797631|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.56% 154 2_CM030788.1_40828017..40844298|unknown|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 67.41% passed 99.68% 155 2_CM030788.1_40861552..40874084|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 70.71% 156 2_CM030788.1_41159055..41170769|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 86.18% 157 2_CM030788.1_41438136..41448953|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 76.36% 158 2_CM030788.1_41884380..41896721|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 88.57% 159 2_CM030788.1_42043157..42056631|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.85% 160 2_CM030788.1_42064940..42076254|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 98.10% 161 2_CM030788.1_42173691..42184627|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.90% 162 2_CM030788.1_42294088..42307393|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 94.91% 163 2_CM030788.1_43972598..43985114|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 91.69% 164 2_CM030788.1_44037465..44046263|unknown|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.96% 165 2_CM030788.1_44316185..44322284|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel_Ty3-RT 61.64% passed 82.20% 166 2_CM030788.1_44349814..44361238|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 91.38% 167 2_CM030788.1_45105773..45118369|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.47% 168 2_CM030788.1_4545353..4557009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.35% 169 2_CM030788.1_45638139..45651416|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 98.25% 170 2_CM030788.1_46121042..46133066|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 98.66% 171 2_CM030788.1_46279645..46290409|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 79.38% passed 36.23% 172 2_CM030788.1_46735899..46750787|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 97.97% 173 2_CM030788.1_4693758..4706916|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 99.34% 174 2_CM030788.1_4709937..4724336|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 68.29% passed 88.49% 175 2_CM030788.1_47112497..47124533|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 75.83% passed 75.25% 176 2_CM030788.1_47389859..47402298|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT 61.42% passed 99.89% 177 2_CM030788.1_47406252..47417865|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.42% passed 99.39% 178 2_CM030788.1_479008..488088|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT 61.64% passed 90.98% 179 2_CM030788.1_4801351..4814738|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 93.04% 180 2_CM030788.1_48557165..48570652|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT 57.43% passed 97.55% 181 2_CM030788.1_49217951..49230037|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT 61.64% passed 99.93%
......
WARNING: 7506 sequences contain more than 50% gaps/ambiguity **** TOTAL 62.37% 7 sequences failed composition chi2 test (p-value<5%; df=19) Hashing sequences took 0.030 wall-clock seconds NOTE: 2_CM030791.1_43627819..43638172|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_11796882..11806899|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_392134..400756|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_12025081..12033683|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_59366905..59378629|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_12242480..12254230|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_14981755..14990290|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_12879039..12887567|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_25018583..25032128|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_13549672..13563181|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_9260856..9272415|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_1453670..1465227|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_18226675..18235295|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_15058058..15066686|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_39278378..39290782|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_1522711..1535116|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_8930128..8940872|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_16958805..16969637|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_36086242..36099596|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_17788862..17798803|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_2756267..2767813|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_1792730..1804262|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_38786434..38795065|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_20187873..20196495|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_2875475..2883998|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_20869356..20877883|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_18067260..18077646|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_2126144..2136464|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_24824355..24837835|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_21788631..21802124|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_24225600..24234256|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_22694941..22703598|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_34889596..34904094|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_26967092..26979598|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_56633949..56645542|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_2990121..3001728|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030794.1_51510846..51522557|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_31209378..31219311|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_39043989..39055702|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_33282147..33293906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10502418..10513681|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_36875300..36886645|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036312.1_23834180..23846196|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_42043157..42056631|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_9101272..9112687|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_4545353..4557009|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_36703494..36715457|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_4693758..4706916|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_27741471..27750564|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_479008..488088|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_50979921..50992328|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_49284537..49296937|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_28837980..28850097|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_49317467..49327011|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030788.1_58211569..58225040|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_51506455..51519906|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10267893..10281008|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_52297442..52310708|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_10204007..10212623|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_53084986..53093615|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_17130032..17141071|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_54623561..54636260|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_56660120..56668987|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030788.1_59379762..59388660|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030796.1_11845407..11857664|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030788.1_630225..642500|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_51699695..51712183|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030788.1_8100639..8113474|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_25448344..25460367|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_8927360..8939322|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_31653244..31664936|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030788.1_9423355..9437417|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_33084819..33090459|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030788.1_9959744..9965388|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_42270484..42279117|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_10869411..10878035|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_7801283..7811632|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_10888133..10901446|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_53728052..53739498|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_11860936..11874700|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_36324553..36338951|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_12865978..12881435|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_38786586..38803879|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_17925336..17938373|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036322.1_18383526..18395206|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_18132212..18147356|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_2533442..2542066|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_18481697..18490327|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_19097781..19109522|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_18768784..18780338|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_30498575..30510616|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_19049470..19061495|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_47458220..47469502|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030789.1_22852618..22863897|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_5841103..5846796|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030789.1_23745342..23751033|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_39202485..39214405|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_24391212..24403127|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_30830392..30843714|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_25054183..25067825|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036312.1_50368352..50380027|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_2716125..2727746|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_24441473..24446975|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030789.1_28713550..28719050|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_46841965..46850730|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_30689264..30697896|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_49066554..49078280|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_30744160..30755932|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_13718944..13730088|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_36717873..36729188|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030795.1_27873991..27885745|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_36850633..36862362|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030794.1_44504583..44515162|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_39180606..39189802|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_41214654..41227885|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_41984936..41998141|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_34583731..34589398|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030789.1_42134700..42141487|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_18364963..18376087|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_43460865..43471455|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_6093880..6107108|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT is identical to 2_CM030789.1_43861508..43874731|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_45557538..45573400|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030789.1_44110431..44122716|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_490090..495147|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Reina_Ty3-RT is identical to 2_CM030789.1_47729189..47734543|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Reina_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030791.1_46638688..46644081|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030789.1_48292748..48298158|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030795.1_17495216..17507148|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030789.1_49369119..49381063|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030789.1_6485976..6499119|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030789.1_49501578..49514656|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_27872130..27883851|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_51416321..51427485|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_25137090..25148518|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_52011160..52019925|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_25435336..25454297|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_52329733..52340827|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_43781928..43791045|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_52449384..52458502|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_32189761..32201930|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_5402353..5414363|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030796.1_2210888..2222403|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_6428429..6440020|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036312.1_32271942..32283667|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_7556769..7568339|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_15844318..15855838|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030789.1_7760045..7771716|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_13820688..13833640|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030789.1_8675023..8688543|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_43431251..43441262|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030789.1_8878619..8888668|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030793.1_12519705..12532071|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT is identical to 2_CM030790.1_10126729..10139159|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_34886062..34895237|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030790.1_1245103..1254191|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030796.1_5728051..5741022|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030790.1_14945283..14956892|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_4205772..4211252|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030790.1_1664753..1670256|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030795.1_45730398..45740421|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT is identical to 2_CM030790.1_1821769..1831796|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/Tekay_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030792.1_39003765..39015325|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030790.1_20626995..20638403|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 2_CM030790.1_24899691..24910531|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT is identical to 2_CM030790.1_22547841..22558679|Gypsy|Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Retand_Ty3-RT but kept for subsequent analysis NOTE: 5_CM036317.1_29190768..29199459|Gypsy|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT is identical to 2_CM030790.1_30276609..30282522|unknown|Class_I/LTR/Ty3_gypsy/chromovirus/CRM_Ty3-RT but kept for subsequent analysis
......
Printing alignment to phylip file ty3.mafft.uniqueseq.phy took 0.044 sec Alignment was printed to ty3.mafft.uniqueseq.phy
For your convenience alignment with unique sequences printed to ty3.mafft.uniqueseq.phy Alignment state count time was 0.024 seconds. Empirical state frequencies: 0.0609755283 0.0565089695 0.0385732441 0.0627584945 0.0256636547 0.0303021098 0.0462902874 0.0627191778 0.0274731368 0.0523020836 0.0900259904 0.0755611059 0.0343947029 0.0647983906 0.0457563119 0.0436825851 0.0499330245 0.0134233633 0.0444040007 0.0744538382 Creating fast initial parsimony tree by random order stepwise addition...
@thomaskf
thomaskf
commented
2 years ago @wensulin93 Is it possible to send me the alignment file for checking the issue? My email address: thomaskf@gmail.com Thanks!
Wenwen012345
commented
2 years ago @thomaskf The mail has been sent.
thomaskf
commented
2 years ago @wensulin93 Thanks for sending us the data. I have checked on my side and the program worked fine. I just noticed that you are using the option "--nt AUTO". It seems that there are 40 CPU threads available in your machine. Using this option may enable IQ-Tree to use all CPU threads. It is fine if you only run one IQ-Tree. However, if you are running two IQ-Trees, then each IQ-Tree may use 40 CPUs and thus the problem occurred. If you are running two IQ-Trees, it is better to specific the amount of CPU threads for each run, like 20 or less (i.e. --nt 20). I guess this may be the possible reason why there is no problem when running one IQ-Tree but there is problem when running two IQ-Trees on the same machine. Moreover, please make sure two IQ-Trees are not processing the same alignment file. Hope this helps.
Wenwen012345
commented
2 years ago Hello! @thomaskf
Thank you for your advice. I guess that might be the problem. Another problem was that my previous evolutionary tree took over 60 hours to build. The current status is like this: Iteration 46 LogL:-220509.858 Time:22h:36m:10s (40h:10m:58s left). It's too long for me to wait. I notice that the.treefile file has been generated. In fact, I just need this file and later beautify the tree. May I directly follow up without waiting for the program to complete? Because it's been too long.
roblanf
commented
2 years ago HI @wensulin93, you should not use the tree file without waiting. IQ-TREE writes the best tree it has found so far to that file. So it may still improve a lot. If you use the tree file before the program completes, you have no guarantee about it being the best estimate of the ML tree.
If you cannot wait for the ML analysis to finish, you should use a different and faster method like Neighbour-Joining, or use simpler models for your ML analysis.
Wenwen012345
commented
2 years ago Ok, thank you very much! @roblanf
Wenwen012345
commented
2 years ago @wensulin93 Thanks for sending us the data. I have checked on my side and the program worked fine. I just noticed that you are using the option "--nt AUTO". It seems that there are 40 CPU threads available in your machine. Using this option may enable IQ-Tree to use all CPU threads. It is fine if you only run one IQ-Tree. However, if you are running two IQ-Trees, then each IQ-Tree may use 40 CPUs and thus the problem occurred. If you are running two IQ-Trees, it is better to specific the amount of CPU threads for each run, like 20 or less (i.e. --nt 20). I guess this may be the possible reason why there is no problem when running one IQ-Tree but there is problem when running two IQ-Trees on the same machine. Moreover, please make sure two IQ-Trees are not processing the same alignment file. Hope this helps.
Yes, that would solve it.
Hello，owner！
As mentioned，when the softeare run to the “Creating fast initial parsimony tree by random order stepwise addition...” step，it just stoped. Notthing happened then. No any information then. But when I changed to my computer (not very fast), it can work. My command is “iqtree2 -s ty1.mafft -bb 1000 -nt AUTO -T 20 -m Q.mammal+F+R5.” Why did this happen?