cannot stat 'ref.fa.LTR.intact.fa.gff3': No such file or directory about edta

[oushujun]

You may need to simplify your sequence IDs. Keep it short, no space or special characters.

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On Mon, Jan 13, 2020, 11:33 PM paperonion ***@***.***> wrote: Hello, I have yesterday started the EDTA pipeline, and I am very excited. However, I get the error that certain LTR files are not present, after 1 hour of run time. Do you know what is going on? I call the script as follows: perl /data/modules/python/python-anaconda2-2019.10-EDTA/envs/EDTA/share/EDTA/EDTA.pl -genome ref.fa -species others -step all -curatedlib library7birds.fa -sensitive -repeatmasker /data/biosoftware/RepeatMasker/RepeatMasker/ 1 -anno 1 -evaluate 1 -t 15 The input library and genome are soft links (ln -s). I then get the following error output: perl rename_LTR.pl genome.fa target_sequence.fa LTR_retriever.defalse cp: cannot stat 'ref.fa.LTR.intact.fa.gff3': No such file or directory cp: cannot stat 'ref.fa.LTRlib.fa': No such file or directory cp: cannot stat 'ref.fa.LTRlib.fa': No such file or directory Error: LTR results not found! ERROR: Raw LTR results not found in ref.fa.EDTA.raw/ref.fa.LTR.raw.fa at /data/modules/python/python-anaconda2-2019.10-EDTA/envs/EDTA/share/EDTA/EDTA.pl line 284. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#42?email_source=notifications&email_token=ABNX4NEFTVAZD6VCFSBOGADQ5VTDDA5CNFSM4KGOLD4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IF662ZA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NGCABJGYW72RR5RX33Q5VTDDANCNFSM4KGOLD4A> .

[peterpru]

Dear Shujun,
I have simplified the fasta headers of the genome as well as the curated library (original headers: CR1-E1_fAlb#LINE/CR1, new headers: CR1-E1_fAlb_LINE-CR1). I am running it now, and will update my progress. Thank you for the fast reply.

[oushujun]

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