ERROR: Raw LTR/TIR/Helitron results not found in *.EDTA.raw/

[sunnycqcn]

I run EDTA pipeline for identifying TE using about 100 fungi isolate genome sequences. All genome sequences were de novo assembly. Around 70% isolates can get good results using EDTA pipeline. However, others can not get. with the error as following: I have tried lots of times.

Mon Dec 9 17:13:26 EST 2019 EDTA_raw: Check files and dependencies, prepare working directories.

Mon Dec 9 17:13:26 EST 2019 Start to find LTR candidates.

Mon Dec 9 17:13:26 EST 2019 Identify LTR retrotransposon candidates from scratch.

awk: fatal: cannot open file `L009.fa.pass.list' for reading (No such file or directory)
Warning: LOC list - is empty.

Error: Error while loading sequencecp: cannot stat ‘L009.fa.LTRlib.fa’: No such file or directory
cp: cannot stat ‘L009.fa.LTRlib.fa’: No such file or directory
Error: LTR results not found!

ERROR: Raw LTR results not found in L009.fa.EDTA.raw/L009.fa.LTR.raw.fa at /home/AAFC-AAC/fuf/EDTA/EDTA.pl line 250.
Did you meet like this error before?
Thanks,
Fuyou

[oushujun]

Dear Fuyou, It's likely some of your genomes do not have LTR or no confident LTR elements could be found. You may want to use -force 1 to get over those categories with no results. Run EDTA.pl for more help info. Best, Shujun

…

On Mon, Dec 9, 2019, 4:23 PM sunnycqcn ***@***.***> wrote: I run EDTA pipeline for identifying TE using about 100 fungi isolate genome sequences. All genome sequences were de novo assembly. Around 70% isolates can get good results using EDTA pipeline. However, others can not get. with the error as following: I have tried lots of times. Mon Dec 9 17:13:26 EST 2019 EDTA_raw: Check files and dependencies, prepare working directories. Mon Dec 9 17:13:26 EST 2019 Start to find LTR candidates. Mon Dec 9 17:13:26 EST 2019 Identify LTR retrotransposon candidates from scratch. awk: fatal: cannot open file `L009.fa.pass.list' for reading (No such file or directory) Warning: LOC list - is empty. Error: Error while loading sequencecp: cannot stat ‘L009.fa.LTRlib.fa’: No such file or directory cp: cannot stat ‘L009.fa.LTRlib.fa’: No such file or directory Error: LTR results not found! ERROR: Raw LTR results not found in L009.fa.EDTA.raw/L009.fa.LTR.raw.fa at /home/AAFC-AAC/fuf/EDTA/EDTA.pl line 250. Did you meet like this error before? Thanks, Fuyou — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#33?email_source=notifications&email_token=ABNX4NHBPU5B7RO7UICY5VDQX3APTA5CNFSM4JYTSIEKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H7JFJXA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NFMGUFDTSCIUSQ7IEDQX3APTANCNFSM4JYTSIEA> .

[oushujun]

Dear Fuyou,

Please let me know if this issue is resolved or still persistent. Also please update your EDTA package as I just posted an official release with more exciting updates. Let me know if you have more questions.

Happy New Year!

Best,
Shujun

[sunnycqcn]

Dear Shujun,
I am much appreciated for your excellent work. The job is running well with your suggestion. But I am not sure the results is correct since my genome is fungal, not rice.
Thanks,
Fuyou

[oushujun]

Dear Fuyou, I tested in rice, maize, and drosophila and the performance is comparable. I have not tested in any fungal genomes tho, due to the lack of curated species. If you know of one, you can benchmark EDTA with the lib_test.pl script in the package. Or you can many curate some random intact elements to get an idea of the correctness. Please let me know if you have other questions. Best, Shujun

…

On Fri, Dec 27, 2019, 9:04 AM sunnycqcn ***@***.***> wrote: Dear Shujun, I am much appreciated for your excellent work. The job is running well with your suggestion. But I am not sure the results is correct since my genome is fungal, not rice. Thanks, Fuyou — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#33?email_source=notifications&email_token=ABNX4NARMW52MU36224KWGTQ2YYQBA5CNFSM4JYTSIEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHXPETI#issuecomment-569307725>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NCDVKB4REOVX4V5MD3Q2YYQBANCNFSM4JYTSIEA> .

[sunnycqcn]

Dear Shujun, I think currently I get good results. Happy new year, Fuyou

…

On Fri, Dec 27, 2019 at 10:20 PM Shujun Ou ***@***.***> wrote: Dear Fuyou, I tested in rice, maize, and drosophila and the performance is comparable. I have not tested in any fungal genomes tho, due to the lack of curated species. If you know of one, you can benchmark EDTA with the lib_test.pl script in the package. Or you can many curate some random intact elements to get an idea of the correctness. Please let me know if you have other questions. Best, Shujun On Fri, Dec 27, 2019, 9:04 AM sunnycqcn ***@***.***> wrote: > Dear Shujun, > I am much appreciated for your excellent work. The job is running well > with your suggestion. But I am not sure the results is correct since my > genome is fungal, not rice. > Thanks, > Fuyou > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > < #33?email_source=notifications&email_token=ABNX4NARMW52MU36224KWGTQ2YYQBA5CNFSM4JYTSIEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHXPETI#issuecomment-569307725 >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABNX4NCDVKB4REOVX4V5MD3Q2YYQBANCNFSM4JYTSIEA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#33?email_source=notifications&email_token=AF3JCKGKHNH5JZFKRBROSQTQ23HXLA5CNFSM4JYTSIEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHYBV6A#issuecomment-569383672>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF3JCKDC3QD3F3B6MVK2HT3Q23HXLANCNFSM4JYTSIEA> .

-- Fuyou Fu, Ph.D. Department of Botany and Plant Pathology Purdue University USA

[oushujun]

Dear @sunnycqcn,

Thank you for your update. If possible, please share your experience or even some of your EDTA results in the "Happy Users" page. It will help others to get confidence and learn to use this method. Thank you for using EDTA! Happy New Year!

Best,
Shujun

[sunnycqcn]

I will do after I finish my all isolate. I have more 160 isolates.
Thanks,
Fuyou

[oushujun]

That's exciting! Look forward to your update.

Best,
Shujun