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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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perl call_seq_by_list.pl is not working #118

Closed Ravindra-Raut closed 1 year ago

Ravindra-Raut commented 2 years ago

Hello Sir I am getting empty output file after using call_seq_by_list.pl I used gt suffixerator, gt ltrharvest, ltr_finder, LTR_retriever and awk '{if ($1~/[0-9]+/) print $10"\t"$1}' to get the output_d file.

perl LTR_retriever/bin/call_seq_by_list.pl O_sativa_Hitomebore_output_d -C O_sativa_Hitomebore.fa > O_sativa_Hitomebore_output_e

Please give some suggestion.

oushujun commented 2 years ago

Please share a sample of your d file. Thanks.

Shujun

On Wed, Apr 6, 2022 at 6:14 AM Ravindra Raut @.***> wrote:

Hello Sir I am getting empty output file after using call_seq_by_list.pl http://call_seq_by_list.pl I used gt suffixerator, gt ltrharvest, ltr_finder, LTR_retriever and awk '{if ($1~/[0-9]+/) print $10"\t"$1}' to get the output_d file.

perl LTR_retriever/bin/call_seq_by_list.pl O_sativa_Hitomebore_output_d -C O_sativa_Hitomebore.fa > O_sativa_Hitomebore_output_e

Please give some suggestion.

— Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/118, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NER74U6TRU4WUVHGU3VDWE2ZANCNFSM5SV7Z4IQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Ravindra-Raut commented 2 years ago

Copia DG000053.1:155936..163480 Gypsy DG000053.1:659820..670468 Copia DG000053.1:831967..838857 Copia DG000053.1:904437..909506 Gypsy DG000053.1:938753..952845 Gypsy DG000053.1:943164..952170 Copia DG000053.1:1607765..1616684 unknown DG000053.1:1875688..1878878 Gypsy DG000053.1:5735020..5740174 Copia DG000053.1:6160933..6166718 Gypsy DG000053.1:7748205..7753658 Gypsy DG000053.1:8507607..8518861 Gypsy DG000053.1:8972535..8976944 Copia DG000053.1:9213590..9219980 unknown DG000053.1:9941351..9943144 Gypsy DG000053.1:9955597..9960000 Copia DG000053.1:10999349..11005799 unknown DG000053.1:11664413..11667808 Copia DG000053.1:13003409..13009850 Copia DG000053.1:13133261..13139434 Gypsy DG000053.1:13590302..13595671 unknown DG000053.1:13761132..13765242 Gypsy DG000053.1:14632814..14645443 Copia DG000053.1:15532938..15539392 Gypsy DG000053.1:16427699..16431226 Gypsy DG000053.1:16539246..16543642 Gypsy DG000053.1:16668829..16674115 Copia DG000053.1:16832110..16838500 Gypsy DG000053.1:16905029..16910569 Copia DG000053.1:16965462..16973878 Gypsy DG000053.1:18605449..18609852 Gypsy DG000053.1:18941822..18949575 Gypsy DG000053.1:19155065..19162467 Copia DG000053.1:19296252..19305470 Copia DG000053.1:19330594..19336121 Copia DG000053.1:19517753..19522960 Gypsy DG000053.1:19918895..19926600 Gypsy DG000053.1:20540525..20549413 unknown DG000053.1:21141732..21143208 Gypsy DG000053.1:21254387..21265709 Gypsy DG000053.1:21421094..21432396 Gypsy DG000053.1:21850661..21862000 Gypsy DG000053.1:22101198..22105676 Gypsy DG000053.1:22423503..22434822 Gypsy DG000053.1:22548526..22553503 Gypsy DG000053.1:23580703..23586641 Copia DG000053.1:23925413..23931864 Gypsy DG000053.1:24031598..24043058 Copia DG000053.1:26405475..26410248 Gypsy DG000053.1:27383129..27394432 Gypsy DG000053.1:27438971..27444185 unknown DG000053.1:29620087..29624772 Copia DG000053.1:29628932..29635363 unknown DG000053.1:30034993..30036745 Copia DG000053.1:30067402..30072586 Copia DG000053.1:30569680..30576117 Gypsy DG000053.1:31519466..31530635 Copia DG000053.1:31611011..31616285 unknown DG000053.1:32530763..32532877 Copia DG000053.1:32851993..32857008 Copia DG000053.1:32963957..32968744 Gypsy DG000053.1:33636727..33641442 Gypsy DG000053.1:34247378..34251757 unknown DG000053.1:34847913..34849560 unknown DG000053.1:34868541..34870188 unknown DG000053.1:35965259..35968372 Gypsy DG000053.1:36700145..36705806 unknown DG000053.1:37762481..37766361 Copia DG000053.1:38857814..38862689 unknown DG000053.1:39551978..39553940 Copia DG000053.1:39902336..39904347 Gypsy DG000053.1:40310636..40321920 Gypsy DG000053.1:41439515..41447944 Gypsy DG000053.1:42143179..42147124 Copia DG000053.1:42621752..42626868 Copia DG000053.1:43373747..43379261 Gypsy DG000053.1:43521394..43526312 Copia DG000054.1:138438..144887 Gypsy DG000054.1:320583..331914 Copia DG000054.1:460607..465566 Copia DG000054.1:1767932..1772817 Copia DG000054.1:2309998..2312147 Copia DG000054.1:2527395..2532694 Copia DG000054.1:3114225..3119471 unknown DG000054.1:3153411..3156325 Copia DG000054.1:3460422..3465906 Gypsy DG000054.1:3897338..3908641 Copia DG000054.1:5382859..5394899 Gypsy DG000054.1:5427913..5439365 Gypsy DG000054.1:6435023..6444644 Copia DG000054.1:6482766..6487427 Copia DG000054.1:7586171..7592588 Gypsy DG000054.1:8071266..8076756 unknown DG000054.1:8178646..8182895 Copia DG000054.1:8357960..8369977 unknown DG000054.1:9064019..9068047 Copia DG000054.1:9103561..9109958 Copia DG000054.1:9176427..9182540 Gypsy DG000054.1:9292243..9296645 Gypsy DG000054.1:9771125..9776635 Gypsy DG000054.1:9943452..9948998 Gypsy DG000054.1:10318546..10326427 Gypsy DG000054.1:10326432..10337914 unknown DG000054.1:10411235..10414147 Gypsy DG000054.1:10610474..10614832 Gypsy DG000054.1:10628339..10639813 unknown DG000054.1:11398354..11400972 Copia DG000054.1:11482313..11491573 Gypsy DG000054.1:11703606..11711148 Gypsy DG000054.1:11877521..11881595 unknown DG000054.1:11915205..11918883 Copia DG000054.1:12097811..12108198 Copia DG000054.1:12731782..12740953 Gypsy DG000054.1:12973179..12979798 Gypsy DG000054.1:14482073..14491291 Copia DG000054.1:15263183..15272106 Gypsy DG000054.1:15351784..15357405 unknown DG000054.1:15712134..15718385 Gypsy DG000054.1:15799319..15803222 Gypsy DG000054.1:15863762..15875381 unknown DG000054.1:15988218..15992923 Gypsy DG000054.1:15993775..16003064 Gypsy DG000054.1:16494300..16501583 Copia DG000054.1:16734614..16739143 Copia DG000054.1:16845165..16851562 Gypsy DG000054.1:16884501..16892044 Gypsy DG000054.1:17120500..17131848 unknown DG000054.1:17592549..17597608 Copia DG000054.1:18277801..18282811 Gypsy DG000054.1:18665387..18674453 unknown DG000054.1:18747764..18751024 Copia DG000054.1:18819928..18825134 Gypsy DG000054.1:19413430..19424279 Gypsy DG000054.1:19712048..19716468 Gypsy DG000054.1:19723936..19729330 Gypsy DG000054.1:19787267..19798471 Gypsy DG000054.1:19862762..19868102 unknown DG000054.1:20259908..20263487 unknown DG000054.1:20676083..20682109 unknown DG000054.1:20917997..20925355 Copia DG000054.1:21149705..21154845 Gypsy DG000054.1:22043651..22049712 Gypsy DG000054.1:22334462..22339511 Gypsy DG000054.1:22946980..22960165 Copia DG000054.1:23624104..23627436 Copia DG000054.1:23784447..23789985 Gypsy DG000054.1:23972142..23978688 unknown DG000054.1:24249862..24252255 Gypsy DG000054.1:24794795..24799147 unknown DG000054.1:24834796..24838743 Gypsy DG000054.1:25887260..25897065 Gypsy DG000054.1:26222557..26227968 Gypsy DG000054.1:27538563..27543966 Gypsy DG000054.1:30388925..30400690 Gypsy DG000054.1:30390663..30397120 Copia DG000054.1:31361457..31364817 unknown DG000054.1:31648931..31653435 Gypsy DG000054.1:32233034..32246107 Copia DG000054.1:33071839..33078281 Gypsy DG000054.1:34160781..34166768 Gypsy DG000054.1:34409332..34412756 unknown DG000054.1:34445842..34449515 Copia DG000054.1:34802912..34808112 Copia DG000055.1:414040..424343 Gypsy DG000055.1:966735..973141 Gypsy DG000055.1:1379848..1391408 Gypsy DG000055.1:2251288..2257956 Copia DG000055.1:3288787..3293659 Copia DG000055.1:4143674..4147602 Gypsy DG000055.1:5051019..5057190 unknown DG000055.1:5313812..5318032 Copia DG000055.1:6733433..6745326 Copia DG000055.1:7199706..7210010 Gypsy DG000055.1:8067910..8079350 Gypsy DG000055.1:8971981..8977475 Gypsy DG000055.1:9046302..9051721 Gypsy DG000055.1:9146316..9152848 Gypsy DG000055.1:10779068..10784474 Gypsy DG000055.1:11342301..11353915 Copia DG000055.1:11359300..11364121 Copia DG000055.1:11651950..11656388 Copia DG000055.1:11749884..11756314 Gypsy DG000055.1:14668570..14680018 unknown DG000055.1:15004942..15007791 Copia DG000055.1:15277284..15282484 Gypsy DG000055.1:15783334..15798483 Gypsy DG000055.1:15893278..15907157 Copia DG000055.1:16643356..16655428 Copia DG000055.1:16705382..16710660 Gypsy DG000055.1:16892129..16904099 Gypsy DG000055.1:17535632..17546918 Gypsy DG000055.1:17646117..17651373 Gypsy DG000055.1:17765978..17770467 Gypsy DG000055.1:17810045..17820992 Copia DG000055.1:18193439..18198563 Copia DG000055.1:18215125..18219898 Gypsy DG000055.1:18276807..18287121 Copia DG000055.1:18361942..18368389 Gypsy DG000055.1:19145293..19152667 Gypsy DG000055.1:19625108..19636805 Copia DG000055.1:19782497..19794154 Copia DG000055.1:19861423..19867857 Gypsy DG000055.1:19890846..19895250 Gypsy DG000055.1:19899118..19908964 Gypsy DG000055.1:20450774..20462732 Gypsy DG000055.1:20529414..20537232 Gypsy DG000055.1:21086909..21100096 Copia DG000055.1:21111429..21116280 Copia DG000055.1:21157834..21163710 Gypsy DG000055.1:21615163..21624016 Copia DG000055.1:21635833..21643497 Gypsy DG000055.1:22070185..22076675 Gypsy DG000055.1:22374134..22382707 unknown DG000055.1:22863214..22874715 Gypsy DG000055.1:22985894..22990241 unknown DG000055.1:23238883..23243614 unknown DG000055.1:23504984..23508264 Copia DG000055.1:23596644..23603077 unknown DG000055.1:24065741..24080026 Copia DG000055.1:25125859..25132263 Copia DG000055.1:25669186..25673997 Copia DG000055.1:25695586..25702238 unknown DG000055.1:26208090..26214324 Gypsy DG000055.1:26485163..26491577 unknown DG000055.1:27109693..27117014 Gypsy DG000055.1:27709588..27713940 Gypsy DG000055.1:28335123..28346339 Gypsy DG000055.1:28555794..28567273 Gypsy DG000055.1:30200019..30205444 Gypsy DG000055.1:30200896..30205435 unknown DG000055.1:30917451..30919872 Gypsy DG000055.1:30941332..30947750 unknown DG000055.1:31522253..31531483 Copia DG000055.1:31523591..31530026 Gypsy DG000055.1:32807092..32811483 Copia DG000055.1:33099854..33105521 Copia DG000055.1:33180827..33187220 Copia DG000055.1:33358601..33367861 Gypsy DG000055.1:33617776..33629093 Gypsy DG000055.1:33659955..33672888 Copia DG000055.1:35145772..35152201 unknown DG000055.1:35641850..35653528 Copia DG000055.1:35846036..35851037 Copia DG000055.1:35992628..35997412 Copia DG000055.1:36575970..36586262 Copia DG000055.1:36746521..36751792 Gypsy DG000055.1:36949125..36960528 Copia DG000055.1:37105877..37110632 Copia DG000056.1:1187021..1193463 Gypsy DG000056.1:1591133..1600272 Copia DG000056.1:1643339..1648143 Gypsy DG000056.1:1790627..1801930 Gypsy DG000056.1:2369694..2380346 Gypsy DG000056.1:2852836..2859267 Gypsy DG000056.1:2890618..2901943 Gypsy DG000056.1:4965241..4978795 Gypsy DG000056.1:4979218..4985429 Gypsy DG000056.1:5496105..5507425 Gypsy DG000056.1:5729019..5733409 Gypsy DG000056.1:5867538..5878839 Gypsy DG000056.1:6016384..6027877 Gypsy DG000056.1:6182336..6187584 Gypsy DG000056.1:6340349..6352032 unknown DG000056.1:6373993..6375578 Gypsy DG000056.1:7099903..7104310 Gypsy DG000056.1:7167417..7178754 Gypsy DG000056.1:7918818..7924422 Gypsy DG000056.1:8943033..8954325 Gypsy DG000056.1:8989401..8994834 Gypsy DG000056.1:8998595..9003003 Gypsy DG000056.1:9039963..9051283 Gypsy DG000056.1:9070649..9078402 Copia DG000056.1:9575457..9581873 Gypsy DG000056.1:9834651..9838929 Gypsy DG000056.1:9894024..9898416 Gypsy DG000056.1:10002368..10006773 Gypsy DG000056.1:10018917..10023207 Gypsy DG000056.1:10033308..10041047 Gypsy DG000056.1:10102532..10106899 Gypsy DG000056.1:10216585..10221029 Gypsy DG000056.1:10438626..10442582 Gypsy DG000056.1:10503981..10508745 Gypsy DG000056.1:10549198..10553562 unknown DG000056.1:10620606..10635264 unknown DG000056.1:10896057..10900096 Gypsy DG000056.1:11290094..11303101 Gypsy DG000056.1:11347662..11357658 Copia DG000056.1:11365117..11371321 Copia DG000056.1:11373333..11379730 unknown DG000056.1:11385408..11388058 Copia DG000056.1:11391290..11400967 unknown DG000056.1:11710912..11712465 Gypsy DG000056.1:12151613..12162918 Gypsy DG000056.1:12335352..12346682 Gypsy DG000056.1:12457445..12463021 Gypsy DG000056.1:12741676..12747202 Gypsy DG000056.1:12775176..12783784 Gypsy DG000056.1:12820327..12834179 Gypsy DG000056.1:13548138..13559465 Gypsy DG000056.1:13846449..13857287 Copia DG000056.1:14359529..14364747 Gypsy DG000056.1:14368131..14379444 Gypsy DG000056.1:14738605..14744625 Gypsy DG000056.1:17341277..17352592 Copia DG000056.1:17678727..17683807 Gypsy DG000056.1:17865802..17876310 Copia DG000056.1:18904797..18911233 Copia DG000056.1:19967684..19979605 unknown DG000056.1:20256328..20260422 Gypsy DG000056.1:20940868..20946084 Copia DG000056.1:22588641..22595501 Gypsy DG000056.1:24174233..24181953 Copia DG000056.1:24535666..24540865 unknown DG000056.1:24649423..24653324 Gypsy DG000056.1:24788981..24792172 Copia DG000056.1:25124142..25129886 Copia DG000056.1:25785549..25794847 Gypsy DG000056.1:26771482..26775721 Gypsy DG000056.1:27583282..27596243 Copia DG000056.1:28742986..28749403 Copia DG000056.1:29155778..29160169 Gypsy DG000056.1:29229715..29236514 unknown DG000056.1:29451427..29455075 Copia DG000056.1:30094131..30100544 Gypsy DG000056.1:30956378..30962611 Gypsy DG000056.1:32228484..32239799 Copia DG000056.1:33279916..33284914 Gypsy DG000056.1:34506825..34512849 Gypsy DG000056.1:35263639..35275090 Gypsy DG000056.1:35352638..35358149 Gypsy DG000056.1:35693877..35705437 Copia DG000057.1:726285..737457 Gypsy DG000057.1:746182..757492 Gypsy DG000057.1:1029277..1040589 unknown DG000057.1:1409619..1412850 Gypsy DG000057.1:1630267..1637484 Gypsy DG000057.1:2032391..2044602 Copia DG000057.1:2232728..2239174 Gypsy DG000057.1:2405016..2416326 Gypsy DG000057.1:2423415..2434718 Gypsy DG000057.1:3392205..3398960 Gypsy DG000057.1:3411349..3416827 Gypsy DG000057.1:4033784..4045079 Gypsy DG000057.1:4737253..4743249 Copia DG000057.1:4754869..4766833 Gypsy DG000057.1:6018846..6029157 Copia DG000057.1:6033952..6039427 Gypsy DG000057.1:6178657..6190446 Copia DG000057.1:6240575..6245816 Copia DG000057.1:7105875..7111065 Gypsy DG000057.1:7305388..7308627 Gypsy DG000057.1:7455849..7460261 Copia DG000057.1:7515373..7520171 Gypsy DG000057.1:7761469..7773110 Gypsy DG000057.1:8087662..8093636 Copia DG000057.1:8264843..8269874 Gypsy DG000057.1:8662103..8668150 Gypsy DG000057.1:9050870..9062172 unknown DG000057.1:9094066..9108363 Gypsy DG000057.1:9509333..9520631 Gypsy DG000057.1:9848409..9860848 Gypsy DG000057.1:10281309..10289288 unknown DG000057.1:10884154..10886692 Gypsy DG000057.1:10966874..10974361 Gypsy DG000057.1:11006171..11018400 Gypsy DG000057.1:11441835..11447116 Gypsy DG000057.1:12090037..12094451 Gypsy DG000057.1:12291555..12300664 Gypsy DG000057.1:12362658..12366971 Gypsy DG000057.1:12392438..12400182 Gypsy DG000057.1:12444964..12449384 Gypsy DG000057.1:12727744..12732152 Gypsy DG000057.1:12766079..12770484 Gypsy DG000057.1:12904557..12914670 Gypsy DG000057.1:13473663..13485034 Gypsy DG000057.1:13552719..13557117 Gypsy DG000057.1:14464202..14472512 Copia DG000057.1:14736468..14741291 Copia DG000057.1:15760022..15770356 Gypsy DG000057.1:15949016..15958034 Copia DG000057.1:16100753..16107092 Copia DG000057.1:17215801..17220590 Copia DG000057.1:17244647..17250987 Gypsy DG000057.1:17473630..17485037 Gypsy DG000057.1:17593800..17604528 Gypsy DG000057.1:18115235..18120569 Gypsy DG000057.1:18313900..18318571 Gypsy DG000057.1:18336729..18348267 Gypsy DG000057.1:18599189..18609826 Copia DG000057.1:18881289..18886602 Gypsy DG000057.1:18913099..18917502 Copia DG000057.1:19476196..19480628 unknown DG000057.1:19512484..19516394 unknown DG000057.1:19630065..19634335 Gypsy DG000057.1:19724491..19735862 Copia DG000057.1:19967563..19973986 Gypsy DG000057.1:21392922..21397265 Copia DG000057.1:21757144..21763578 Gypsy DG000057.1:21959761..21969856 Gypsy DG000057.1:22526963..22532882 Copia DG000057.1:23551292..23556140 Gypsy DG000057.1:24318653..24323109 unknown DG000057.1:24343341..24346247 Gypsy DG000057.1:24602616..24613896 Gypsy DG000057.1:25072032..25083323 Gypsy DG000057.1:25299944..25311147 Copia DG000057.1:26303808..26308616 Copia DG000057.1:26495738..26500653 Gypsy DG000057.1:27301756..27313401 Copia DG000057.1:27583220..27588339 Copia DG000057.1:27724537..27729547 Copia DG000057.1:28533038..28539450 Copia DG000057.1:28572417..28578858 Copia DG000057.1:28721672..28726421 Copia DG000057.1:29391079..29397512 Copia DG000057.1:29464802..29471218 unknown DG000058.1:556184..563388 unknown DG000058.1:1003168..1005121 Gypsy DG000058.1:2342105..2347749 Gypsy DG000058.1:2928002..2931153 Gypsy DG000058.1:3730580..3744267 Copia DG000058.1:4287984..4294407 Gypsy DG000058.1:4557062..4561773 unknown DG000058.1:5133866..5138179 Gypsy DG000058.1:5964448..5969049 Gypsy DG000058.1:6937001..6948347 Gypsy DG000058.1:7194960..7200632 Copia DG000058.1:7387594..7392658 Copia DG000058.1:7468718..7473517 Gypsy DG000058.1:8825948..8831586 unknown DG000058.1:9185357..9188476 Gypsy DG000058.1:9454218..9458638 Gypsy DG000058.1:10830639..10844441 Gypsy DG000058.1:11677777..11683937 Gypsy DG000058.1:12459350..12470815 Gypsy DG000058.1:13200589..13209873 Gypsy DG000058.1:14163315..14170693 Gypsy DG000058.1:14170995..14181771 Copia DG000058.1:14322959..14329376 unknown DG000058.1:14404170..14413840 Gypsy DG000058.1:14550708..14562244 Gypsy DG000058.1:14606072..14608853 Gypsy DG000058.1:14799700..14807444 Gypsy DG000058.1:14924802..14934351 Gypsy DG000058.1:15203909..15211656 Copia DG000058.1:15225644..15232021 Gypsy DG000058.1:15243772..15248178 Gypsy DG000058.1:16332237..16336648 Gypsy DG000058.1:16462262..16472561 Gypsy DG000058.1:16481600..16489210 unknown DG000058.1:16514644..16519380 Copia DG000058.1:16971347..16976532 Gypsy DG000058.1:17037241..17041589 Gypsy DG000058.1:17623538..17627588 unknown DG000058.1:17642620..17645293 Gypsy DG000058.1:17778544..17786217 Copia DG000058.1:17851556..17857716 Gypsy DG000058.1:17936823..17942796 Gypsy DG000058.1:17958420..17969721 Copia DG000058.1:18013034..18016824 Gypsy DG000058.1:18104850..18115460 Gypsy DG000058.1:18200147..18213874 Gypsy DG000058.1:19006331..19011334 Gypsy DG000058.1:19881308..19887794 Gypsy DG000058.1:20241480..20252794 Gypsy DG000058.1:20257105..20268469 Gypsy DG000058.1:20589008..20600301 Gypsy DG000058.1:20808111..20819025 Gypsy DG000058.1:21077478..21087460 Copia 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unknown DG000059.1:7328457..7332557 Copia DG000059.1:7389534..7396003 Gypsy DG000059.1:7538984..7552804 Gypsy DG000059.1:7595886..7605176 Copia DG000059.1:7802057..7811698 Gypsy DG000059.1:7802758..7806923 Copia DG000059.1:8258095..8262751 Copia DG000059.1:8821154..8827484 Copia DG000059.1:8828469..8834826 Gypsy DG000059.1:9539447..9545509 Gypsy DG000059.1:9688266..9699534 Copia DG000059.1:10027523..10032310 Copia DG000059.1:10055552..10062009 unknown DG000059.1:10859211..10863962 Copia DG000059.1:11031989..11038347 Gypsy DG000059.1:11073470..11084211 Gypsy DG000059.1:11519976..11525438 Gypsy DG000059.1:11567592..11574311 Copia DG000059.1:12049446..12055897 unknown DG000059.1:12257422..12263889 Gypsy DG000059.1:12283271..12287674 Gypsy DG000059.1:12348921..12353335 Gypsy DG000059.1:12458668..12463029 Gypsy DG000059.1:13045303..13049672 Gypsy DG000059.1:13216309..13223512 Copia DG000059.1:13264643..13275303 Gypsy DG000059.1:13672012..13684238 Copia DG000059.1:13746319..13758354 Copia 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DG000059.1:20649651..20655324 unknown DG000059.1:20716352..20719981 Gypsy DG000059.1:21341386..21346924 Gypsy DG000059.1:21909619..21916174 Copia DG000059.1:22339470..22345866 Gypsy DG000059.1:22396696..22402353 Copia DG000059.1:22653440..22657847 Gypsy DG000059.1:22685625..22692703 Copia DG000059.1:22820293..22826724 Gypsy DG000059.1:23363825..23375236 unknown DG000059.1:23485000..23486714 Copia DG000059.1:24146048..24150850 Copia DG000059.1:24434233..24440630 Copia DG000059.1:25455148..25460503 Copia DG000059.1:26233254..26239674 Gypsy DG000059.1:27227900..27239189 Gypsy DG000059.1:27522257..27533546 unknown DG000059.1:27594357..27597501 Copia DG000059.1:27748513..27753588 Gypsy DG000059.1:27915063..27926359 Gypsy DG000059.1:29170759..29182054 Gypsy DG000059.1:29322997..29328645 Copia DG000059.1:29471828..29476642 Copia DG000059.1:30026415..30029723 Gypsy DG000060.1:1302387..1308047 Copia DG000060.1:1467196..1472363 Gypsy DG000060.1:1487965..1499277 Copia DG000060.1:1847090..1852077 Gypsy DG000060.1:1866100..1877510 Copia DG000060.1:1943421..1949828 Copia DG000060.1:2555369..2565647 Gypsy DG000060.1:2645177..2656487 Copia DG000060.1:2663934..2670331 unknown DG000060.1:2757666..2759609 unknown DG000060.1:3788444..3790921 Gypsy DG000060.1:3790976..3796865 Copia DG000060.1:3821678..3828070 Copia DG000060.1:3850300..3856238 Gypsy DG000060.1:4022188..4032778 Copia DG000060.1:4423803..4429242 Copia DG000060.1:4791645..4798056 Gypsy DG000060.1:5082139..5093417 Gypsy DG000060.1:5290597..5302575 Copia DG000060.1:5506569..5515839 unknown DG000060.1:5658476..5660247 Gypsy DG000060.1:5823398..5834715 Gypsy DG000060.1:5893306..5904588 Copia DG000060.1:5905188..5914400 Gypsy DG000060.1:5944274..5949834 Gypsy DG000060.1:6144008..6150906 Gypsy DG000060.1:6327271..6333281 Copia DG000060.1:6340149..6345528 Gypsy DG000060.1:6425252..6429074 Gypsy DG000060.1:6431412..6434130 Gypsy DG000060.1:6657744..6664365 Gypsy DG000060.1:7306140..7317408 Gypsy DG000060.1:7673867..7685264 Copia 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DG000060.1:13272559..13280177 Gypsy DG000060.1:13342383..13352882 Gypsy DG000060.1:13364566..13372183 Gypsy DG000060.1:13533891..13544590 Gypsy DG000060.1:13548138..13555892 Gypsy DG000060.1:13613852..13622130 Gypsy DG000060.1:13679895..13684273 unknown DG000060.1:13948255..13950256 Gypsy DG000060.1:14136118..14139399 Copia DG000060.1:14302970..14309399 Gypsy DG000060.1:15688187..15693426 Gypsy DG000060.1:15887880..15899288 Gypsy DG000060.1:16093377..16100636 Copia DG000060.1:16224993..16231422 Gypsy DG000060.1:16737761..16749051 Gypsy DG000060.1:16758780..16770072 Gypsy DG000060.1:17014562..17025978 unknown DG000060.1:17251386..17255819 Gypsy DG000060.1:17576787..17590292 Gypsy DG000060.1:17651998..17656436 Gypsy DG000060.1:18197905..18207107 Copia DG000060.1:18210345..18215591 Gypsy DG000060.1:18468598..18479886 Copia DG000060.1:18502671..18507875 Gypsy DG000060.1:18556831..18561275 Copia DG000060.1:18726945..18733297 Gypsy DG000060.1:19009928..19015524 Gypsy 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DG000061.1:6080168..6089127 Gypsy DG000061.1:6742453..6753746 Copia DG000061.1:7063338..7068351 Gypsy DG000061.1:7338628..7349968 Gypsy DG000061.1:7400906..7409261 unknown DG000061.1:7792280..7795996 Gypsy DG000061.1:7881722..7888987 Gypsy DG000061.1:8465819..8471382 Copia DG000061.1:8688246..8693028 Gypsy DG000061.1:8753974..8759484 Copia DG000061.1:9165594..9176187 Gypsy DG000061.1:9367731..9378024 Gypsy DG000061.1:9475955..9487279 Gypsy DG000061.1:9794411..9805774 Gypsy DG000061.1:9881938..9887455 Gypsy DG000061.1:9925967..9936194 Gypsy DG000061.1:10912693..10921581 Copia DG000061.1:11029800..11035059 Gypsy DG000061.1:11503143..11508419 Copia DG000061.1:12152144..12161330 Copia DG000061.1:12515140..12519864 Copia DG000061.1:12789764..12794685 Copia DG000061.1:13268761..13275176 Copia DG000061.1:13332904..13339302 Gypsy DG000061.1:13509545..13520897 Gypsy DG000061.1:13734397..13745703 Gypsy DG000061.1:14161537..14172837 Copia DG000061.1:14351482..14357957 Gypsy DG000061.1:16680998..16686457 Copia DG000061.1:17102713..17107551 Gypsy DG000061.1:17502824..17508926 Copia DG000061.1:18141194..18151525 Copia DG000061.1:18765370..18770170 Gypsy DG000061.1:19428127..19435098 Gypsy DG000061.1:19745436..19753418 Gypsy DG000061.1:19754252..19767112 unknown DG000061.1:21292865..21299023 Copia DG000061.1:21580430..21586859 unknown DG000061.1:22653239..22654962 Copia DG000061.1:22706609..22708717 Gypsy DG000062.1:554893..559328 Gypsy DG000062.1:560116..573574 unknown DG000062.1:825822..830302 Gypsy DG000062.1:956837..969838 Copia DG000062.1:1056169..1058715 unknown DG000062.1:1812429..1816191 Gypsy DG000062.1:1965779..1976690 Gypsy DG000062.1:1978154..1985423 Copia DG000062.1:2214107..2218875 unknown DG000062.1:2496111..2500039 unknown DG000062.1:3001733..3003547 Gypsy DG000062.1:4611462..4615671 unknown DG000062.1:4765344..4771402 unknown DG000062.1:5524538..5526189 Gypsy DG000062.1:6611509..6622829 Gypsy DG000062.1:7087347..7098647 Gypsy 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DG000062.1:15912530..15916733 Copia DG000062.1:16048217..16054638 Copia DG000062.1:16360906..16365685 unknown DG000062.1:18591017..18595489 Copia DG000062.1:18705567..18710673 Copia DG000062.1:18787031..18791458 Copia DG000062.1:19118658..19125056 unknown DG000062.1:19267536..19270471 Copia DG000062.1:20001676..20008073 Copia DG000062.1:20152185..20158606 Gypsy DG000062.1:20292077..20297764 unknown DG000062.1:20350954..20353146 Gypsy DG000062.1:21990540..22001841 Gypsy DG000062.1:22469019..22474945 Gypsy DG000062.1:23615104..23620601 Copia DG000063.1:45939..51138 unknown DG000063.1:431624..433281 Gypsy DG000063.1:815083..820002 Copia DG000063.1:1036262..1042706 Copia DG000063.1:1496427..1504114 Gypsy DG000063.1:1942797..1947246 Copia DG000063.1:1954843..1964423 unknown DG000063.1:2305934..2310402 Copia DG000063.1:2699866..2705032 Copia DG000063.1:3167328..3176210 Copia DG000063.1:3434056..3439242 Copia DG000063.1:3959069..3968356 Copia DG000063.1:4127205..4132267 Gypsy DG000063.1:4518349..4525645 Gypsy DG000063.1:4957880..4970888 Gypsy DG000063.1:7374411..7385835 Gypsy DG000063.1:8111946..8122476 Copia DG000063.1:8182822..8187998 Gypsy DG000063.1:8492669..8503953 Gypsy DG000063.1:8534143..8543283 Copia DG000063.1:9623709..9630194 Copia DG000063.1:9740616..9745357 Gypsy DG000063.1:10073865..10081359 Copia DG000063.1:10252582..10259042 unknown DG000063.1:10677579..10682116 Copia DG000063.1:11035151..11041585 Gypsy DG000063.1:11213893..11225855 Gypsy DG000063.1:11285714..11297166 Gypsy DG000063.1:11750907..11756086 Gypsy DG000063.1:12112427..12116833 Gypsy DG000063.1:14907715..14912133 Gypsy DG000063.1:14913526..14927359 Copia DG000063.1:15111426..15119101 Gypsy DG000063.1:15191727..15196079 Gypsy DG000063.1:15470911..15475325 unknown DG000063.1:15487140..15494360 Gypsy DG000063.1:15683916..15688046 Gypsy DG000063.1:15729597..15737342 Gypsy DG000063.1:15961825..15976770 Gypsy DG000063.1:16335399..16346704 Gypsy DG000063.1:16784325..16798100 Gypsy DG000063.1:16870655..16881694 unknown DG000063.1:16912556..16916826 Gypsy DG000063.1:17540448..17546050 Gypsy DG000063.1:17737929..17742309 Gypsy DG000063.1:17786806..17798168 Copia DG000063.1:18064949..18071377 Gypsy DG000063.1:18376303..18387927 Copia DG000063.1:18691108..18696739 Gypsy DG000063.1:18733673..18744977 Gypsy DG000063.1:18756319..18767236 Gypsy DG000063.1:19234951..19242614 Gypsy DG000063.1:19280957..19293494 unknown DG000063.1:19452146..19456145 Gypsy DG000063.1:19502229..19513823 Gypsy DG000063.1:20162844..20174056 Copia DG000063.1:20855233..20861664 Copia DG000063.1:20941481..20947909 Gypsy DG000063.1:21034312..21039782 unknown DG000063.1:21519850..21527196 Gypsy DG000063.1:21689363..21701084 unknown DG000063.1:21894142..21895949 Gypsy DG000063.1:22836962..22842601 Copia DG000063.1:23068503..23073620 Copia DG000063.1:23087556..23092891 unknown DG000063.1:23338721..23341952 unknown DG000063.1:23568159..23569916 unknown DG000063.1:23584723..23588860 Gypsy DG000063.1:23939191..23944636 Gypsy DG000063.1:24142568..24156021 Gypsy DG000063.1:24911452..24916793 unknown DG000063.1:25380420..25386218 unknown DG000063.1:25480549..25482459 unknown DG000063.1:25648112..25654241 Copia DG000063.1:25720568..25732137 Gypsy DG000063.1:26219586..26231533 Gypsy DG000063.1:26938002..26949424 Gypsy DG000063.1:27265809..27277102 Gypsy DG000063.1:27679235..27690537 Gypsy DG000063.1:27865736..27878963 Copia DG000063.1:27926358..27934355 unknown DG000063.1:28272758..28274759 Copia DG000063.1:28276895..28281281 Gypsy DG000063.1:28821344..28832643 Gypsy DG000063.1:28989531..28993216 Copia DG000063.1:29300794..29305225 Copia DG000064.1:44349..49549 Copia DG000064.1:281983..288639 Gypsy DG000064.1:589078..593995 Gypsy DG000064.1:666401..673130 unknown DG000064.1:1313245..1314483 Copia DG000064.1:1572266..1577104 Copia DG000064.1:1822253..1828682 Copia DG000064.1:1954500..1960930 Copia DG000064.1:2353111..2358623 Copia DG000064.1:2353124..2358623 Copia DG000064.1:2369152..2374398 Copia DG000064.1:2526376..2531299 Copia DG000064.1:2551943..2561149 Gypsy DG000064.1:3042401..3053772 unknown DG000064.1:4092333..4095322 unknown DG000064.1:4789773..4794143 Gypsy DG000064.1:4967269..4980976 Gypsy DG000064.1:5225972..5237270 Gypsy DG000064.1:5528576..5542309 unknown DG000064.1:5562181..5565106 Copia DG000064.1:7873057..7880741 Gypsy DG000064.1:8122114..8133432 Copia DG000064.1:8641570..8648016 unknown DG000064.1:8812208..8813691 Copia DG000064.1:8879523..8881534 Gypsy DG000064.1:9012734..9021210 Gypsy DG000064.1:9055752..9067137 Gypsy DG000064.1:9222559..9236385 Copia DG000064.1:9414892..9419616 unknown DG000064.1:9445915..9448696 unknown DG000064.1:9822253..9826371 Gypsy DG000064.1:9853093..9864397 Copia DG000064.1:9995800..10002198 Gypsy DG000064.1:10005693..10017504 Gypsy DG000064.1:10164320..10175599 Gypsy DG000064.1:10397597..10403066 Copia DG000064.1:10753921..10760340 unknown DG000064.1:10937122..10939790 Gypsy DG000064.1:10994658..11002145 Gypsy DG000064.1:11559373..11568663 Gypsy DG000064.1:11786293..11796498 Gypsy DG000064.1:12264190..12268594 Gypsy DG000064.1:12488041..12492775 Gypsy DG000064.1:12652839..12661531 Gypsy DG000064.1:13285178..13296461 Gypsy DG000064.1:13744933..13756216 Gypsy DG000064.1:13822696..13828168 Copia DG000064.1:13958562..13964031 Gypsy DG000064.1:14094824..14099972 Copia DG000064.1:14324024..14328671 Gypsy DG000064.1:14495887..14501193 Copia DG000064.1:14627736..14634174 Gypsy DG000064.1:15225924..15231344 Copia DG000064.1:15409330..15414394 Copia DG000064.1:15656525..15662922 Copia DG000064.1:16303051..16308174 Gypsy DG000064.1:16488489..16499839 Copia DG000064.1:16507387..16513823 unknown DG000064.1:16668534..16673193 unknown DG000064.1:16683519..16686596 Gypsy DG000064.1:16795805..16807101 Gypsy DG000064.1:16818282..16830000 Gypsy DG000064.1:17436501..17447807 Gypsy DG000064.1:18312594..18323427 Gypsy DG000064.1:18394052..18406200 Copia DG000064.1:18528664..18533722 unknown DG000064.1:18779183..18781077 Gypsy DG000064.1:18925117..18936436 Gypsy DG000064.1:19076721..19082164 Copia DG000064.1:19386167..19390876 Gypsy DG000064.1:20281417..20286865 Gypsy DG000064.1:20312149..20323444 Copia DG000064.1:21106262..21112641 Gypsy DG000064.1:21233844..21248387 Copia DG000064.1:21253787..21258499 Copia DG000064.1:21450966..21456167 Copia DG000064.1:21973119..21978193 Gypsy DG000064.1:23071740..23083061 unknown DG000064.1:23986390..23988335 Copia DG000064.1:24277983..24284399 Gypsy DG000064.1:24311048..24320823 Gypsy DG000064.1:24586855..24598143 Copia DG000064.1:24726033..24732468 Gypsy DG000064.1:25175323..25178438 Copia DG000064.1:25581900..25588279 Copia DG000064.1:25746237..25752662 Gypsy DG000064.1:25993278..25998661 Gypsy DG000064.1:25993792..26001422 Gypsy DG000064.1:26006182..26012570 unknown DG000064.1:26505625..26508758 Gypsy DG000064.1:27368236..27373884 Copia DG000064.1:27565949..27570869

Ravindra-Raut commented 2 years ago

Above is the output_d file

Ravindra-Raut commented 2 years ago

I am using protocol by https://github.com/clavia96/LTR_retrotransposon/blob/main/Codes

oushujun commented 2 years ago

Thanks for sharing the file. It looks correctly formatted. you may want to check your genome sequence IDs and see if they match.

Thanks, Shujun

Wenwen012345 commented 2 years ago

Hello, buddy! I had the same problem as you. But I found that simply adding a ".mod" suffix to the genome solved the problem. The script can only run with a. Mod file. Is the O_sativa_Hitomebore. Fa. Mod.

@Ravindra-Raut

Ravindra-Raut commented 2 years ago

Thank you very much @wensulin93. It worked !!!!!

oushujun commented 2 years ago

I am not sure how the problem is solved, but I am glad that it works for you. I am providing a small example here that works for me: perl ~/bin/LTR_retriever/bin/call_seq_by_list.pl genome.fa.retriever.scn.list -C genome.fa > test

The following file has inputs and outputs: test.zip

Let me know if it does not work for you.