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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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No candidate is found in the file(s) you specified. #135

Closed cherryDAP closed 1 year ago

cherryDAP commented 1 year ago

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.

oushujun commented 1 year ago

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

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 https://github.com/oushujun/LTR_retriever/issues/135, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBU5LQPI7UTA2J3PZTV6QQ6JANCNFSM6AAAAAAQOCPHSI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

cherryDAP commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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?

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 https://github.com/oushujun/LTR_retriever/issues/135#issuecomment-1252029818, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGD775ORC2GMQJTVCLV7F2DLANCNFSM6AAAAAAQOCPHSI . You are receiving this because you commented.Message ID: @.***>

cherryDAP commented 1 year ago

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. edcc29915def4a0c8019eefe1b678c4

oushujun commented 1 year ago

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

Shujun

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

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oushujun commented 1 year ago

@cherryDAP any luck?