No candidate is found in the file(s) you specified. about ltr_retriever

[oushujun]

Can you post a couple of lines of the file "ocu.finder.scn"? Thanks

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On Fri, Sep 16, 2022 at 3:48 AM cherryDAP ***@***.***> wrote: After using LTR-FINDER to get ocu.finder.scn, run LTR_retriever. LTR_retriever -threads 10 -genome new.genome.fasta -infinder ocu.finder.scn. But I get the title error: ERROR: No candidate is found in the file(s) you specified. — Reply to this email directly, view it on GitHub <#135>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NBU5LQPI7UTA2J3PZTV6QQ6JANCNFSM6AAAAAAQOCPHSI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[cherryDAP]

A few lines of code for the file "ocu.finder.scn" are as follows, and upload ocu.finder.scn under the code

Program : LTR_FINDER
Version : 1.07

Predict protein Domains 0.025 second

Sequence: fra_scf_24 Len:161586
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] fra_scf_24 15647-22374 331,331 6728 CCTTT N-N 15978-15992 N-N N-N N-N N-N - 6 0.5,0.5 0.979
[ 2] fra_scf_24 23304-27881 336,336 4578 AATAT N-N 23640-23654 N-N N-N N-N N-N - 6 0.486,0.557 1

Predict protein Domains 0.007 second

Sequence: scf_1309 Len:32478
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] scf_1309 4096-9570 603,607 5475 CTTTG N-N 8948-8962 N-N N-N N-N N-N + 6 0.543,0.443 0.988

Predict protein Domains 0.034 second

Sequence: scf_1302 Len:321473
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] scf_1302 171712-179314 823,823 7603 CCTT N-N 172535-172549 N-N N-N N-N N-N - 6 0.514,0.557 0.995

Predict protein Domains 0.000 second

Sequence: scf_1305 Len:9455
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
No LTR Retrotransposons Found

Predict protein Domains 0.000 second

Sequence: scf_1498 Len:2279
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
No LTR Retrotransposons Found

Predict protein Domains 0.039 second

Sequence: scf_1714 Len:164517
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] scf_1714 9763-17883 561,561 8121 CTAAA N-N 10327-10341 N-N N-N N-N N-N - 6 0.486,0.486 0.995
[ 2] scf_1714 33035-37925 419,422 4891 AAGT N-N 37412-37426 N-N N-N N-N N-N + 6 0.414,0.457 0.898
[ 3] scf_1714 60801-74350 234,128 13550 AAAAT N-N 74134-74148 N-N N-N N-N N-N + 6 0.714,0.4 0.798
[ 4] scf_1714 61043-66788 163,163 5746 AAAA N-N 66572-66586 N-N N-N N-N N-N + 6 0.414,0.414 0.951

Predict protein Domains 0.000 second

Sequence: scf_956 Len:3987
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
No LTR Retrotransposons Found

Predict protein Domains 0.000 second

Sequence: scf_1206 Len:175
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
No LTR Retrotransposons Found

Predict protein Domains 0.034 second

Sequence: scf_955 Len:142851
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] scf_955 3073-8688 638,638 5616 ACTTT N-N 7994-8008 N-N N-N N-N N-N + 6 0.529,0.571 0.939
[ 2] scf_955 16583-34716 168,163 18134 N N-N 34504-34518 31109-31594 N-N N-N N-N + 6 0.429,0.471 0.85

Predict protein Domains 0.041 second

Sequence: scf_1209 Len:155082
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] scf_1209 74620-82005 971,970 7386 TATA N-N 81021-81035 N-N N-N N-N N-N + 6 0.5,0.471 0.999
[ 2] scf_1209 107997-116323 617,617 8327 CATA N-N 115654-115668 N-N N-N N-N N-N + 6 0.557,0.543 1
[ 3] scf_1209 140711-146669 725,725 5959 GTGGC N-N 145892-145906 N-N N-N N-N N-N + 6 0.514,0.514 1

Predict protein Domains 0.014 second

Sequence: fra_scf_118 Len:84349
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] fra_scf_118 2740-7205 267,267 4466 TTATG N-N 3046-3060 N-N N-N N-N N-N - 6 0.6,0.486 0.989

Predict protein Domains 0.032 second

Sequence: fra_scf_110 Len:255309
index SeqID Location LTR len Inserted element len TSR PBS PPT RT IN (core) IN (c-term) RH Strand Score Sharpness Similarity
[ 1] fra_scf_110 220093-227182 381,381 7090 TATATA N-N 226787-226801 223604-224029 N-N N-N N-N + 7 0.571,0.543 0.995

Predict protein Domains 0.000 second

ocu.finder.scn.txt

[cherryDAP]

Is there something wrong with my input file, but I am running ltr_finder with default parameters
$ ltr_finder -C -w 2 new.genome.fasta >ocu.finder.scn

[oushujun]

It looks good to me. Can you rerun it and double check if the genome and LTR candidates are from the same version of sequence?

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On Tue, Sep 20, 2022 at 4:41 AM cherryDAP ***@***.***> wrote: Is there something wrong with my input file, but I am running ltr_finder with default parameters $ ltr_finder -C -w 2 new.genome.fasta >ocu.finder.scn — Reply to this email directly, view it on GitHub <#135 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NGD775ORC2GMQJTVCLV7F2DLANCNFSM6AAAAAAQOCPHSI> . You are receiving this because you commented.Message ID: ***@***.***>

[cherryDAP]

Thank you for your suggestion. According to your suggestion, I re-calculated ltr_finder and LTR_retrieverd, and also determined that the genome is the same genome. But unfortunately still the same result.

[oushujun]

Can you test on an Arabidopsis genome or something small and quick? Shujun

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On Wed, Sep 21, 2022 at 7:43 AM cherryDAP ***@***.***> wrote: Thank you for your suggestion. According to your suggestion, I re-calculated ltr_finder and LTR_retrieverd, and also determined that the genome is the same genome. But unfortunately still the same result. [image: edcc29915def4a0c8019eefe1b678c4] <https://user-images.githubusercontent.com/110672898/191495297-7110eb42-b1bf-4be2-a53c-cb0c4e739888.png> — Reply to this email directly, view it on GitHub <#135 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NGRGMHZXWTKZH4XZL3V7LYHRANCNFSM6AAAAAAQOCPHSI> . You are receiving this because you commented.Message ID: ***@***.***>

[oushujun]

@cherryDAP any luck?