ERROR: Stage 1 library not found in chr1.fa.mod.EDTA.combine/chr1.fa.mod.LTR.TIR.Helitron.fa.stg1 at EDTA.pl line 384. #50
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The usage changed a little bit. You need to use two dashes for each long
parameter. Please also update to v1.7.7. Let me know if you have the issue.
…On Wed, Jan 29, 2020, 11:14 AM Tkastylevsky ***@***.***> wrote:
Hello,
I am trying to use EDTA in order to annotate an avian genome(as a test I
do it on a single chromosome), but i keep running into an error :
here is the copy of what I execute in order to run your script :
PATH=$PATH:/home/tkastylevsky/EDTA
cd
cd /home/tkastylevsky/FASTA_files/EDTA/gallus_gallus/chr1/
EDTA.pl -genome /home/tkastylevsky/FASTA_files/EDTA/gallus_gallus/chr1/chr1.fa -anno 1 -force 1
(I tried to add the force 1 based on a solved issue on this github but it
didn't help)
and this is what I get (some of it is in french, sorry, feel free to ask
me if you need any translation, at first glance it seemed to me that
everything was roughly understandable) :
########################################################
Extensive de-novo TE Annotator (EDTA) v1.7.6 Shujun Ou (
***@***.***)
########################################################
mercredi 29 janvier 2020, 18:08:10 (UTC+0100) Dependency checking:
All passed!
mercredi 29 janvier 2020, 18:08:20 (UTC+0100) Obtain raw TE libraries
using various structure-based programs:
At least 1 parameter mandatory:
1. Input fasta file: --genome
Obtain raw TE libraries using various structure-based programs
perl EDTA_raw.pl [options]
--genome [File] The genome FASTA
--species [rice|maize|others] Specify the species for identification of
TIR candidates. Default: others
--type [ltr|tir|helitron|all] Specify which type of raw TE candidates you
want to get. Default: all
--overwrite [0|1] If previous results are found, decide to overwrite (1,
rerun) or not (0, default).
--threads|-t [int] Number of theads to run this script. Default: 4
--help|-h Display this help info
cat: chr1.fa.mod.LTR.intact.fa: Aucun fichier ou dossier de ce type
cat: chr1.fa.mod.TIR.intact.fa: Aucun fichier ou dossier de ce type
cat: chr1.fa.mod.Helitron.intact.fa: Aucun fichier ou dossier de ce type
cat: chr1.fa.mod.LTR.intact.fa.gff3: Aucun fichier ou dossier de ce type
cat: chr1.fa.mod.TIR.intact.fa.gff: Aucun fichier ou dossier de ce type
cat: chr1.fa.mod.Helitron.intact.fa.gff: Aucun fichier ou dossier de ce
type
perl bed2gff.pl EDTA.TE.combo.bed
mv: impossible d'évaluer 'chr1.fa.mod.EDTA.intact.bed.gff': Aucun fichier
ou dossier de ce type
cp: impossible d'évaluer 'chr1.fa.mod.EDTA.intact.gff': Aucun fichier ou
dossier de ce type
mercredi 29 janvier 2020, 18:08:20 (UTC+0100) Obtain raw TE libraries
finished.
All intact TEs found by EDTA:
chr1.fa.mod.EDTA.intact.fa
chr1.fa.mod.EDTA.intact.gff
mercredi 29 janvier 2020, 18:08:20 (UTC+0100) Perform EDTA advcance
filtering for raw TE candidates and generate the stage 1 library:
Genome file chr1.fa.mod not exists!
Perform EDTA basic and advcanced filterings for raw TE candidates and
generate the stage 1 library
perl EDTA_processF.pl [options]
-genome [File] The genome FASTA
-ltr [File] The raw LTR library FASTA
-tir [File] The raw TIR library FASTA
-helitron [File] The raw Helitron library FASTA
-mindiff_ltr [float] The minimum fold difference in richness between LTRs
and contaminants (default: 1)
-mindiff_tir [float] The minimum fold difference in richness between TIRs
and contaminants (default: 1)
-mindiff_hel [float] The minimum fold difference in richness between
Helitrons and contaminants (default: 4)
-repeatmasker [path] The directory containing RepeatMasker (default: read
from ENV)
-blast [path] The directory containing Blastn (default: read from ENV)
-protlib [File] Protein-coding aa sequences to be removed from TE
candidates. (default lib: alluniRefprexp082813 (plant))
You may use uniprot_sprot database available from here:
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/
-threads|-t [int] Number of theads to run this script
-help|-h Display this help info
ERROR: Stage 1 library not found in
chr1.fa.mod.EDTA.combine/chr1.fa.mod.LTR.TIR.Helitron.fa.stg1 at
/home/tkastylevsky/EDTA/EDTA.pl line 384.
I know, through other annotation methods (repeatmodeler) that there are
LTR, TIR and helitrons on this chromosome.
Thank you in advance,
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Done both and it is currently running ! Looks good ! Thanks ! |
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Hello,
I am trying to use EDTA in order to annotate an avian genome(as a test I do it on a single chromosome), but i keep running into an error.
I have installed it with conda, following the script you have on github.
here is the copy of what I execute in order to run your script :
(I tried to add the force 1 based on a solved issue on this github but it didn't help)
and this is what I get (some of it is in french, sorry, feel free to ask me if you need any translation, at first glance it seemed to me that everything was roughly understandable) :
I know, through other annotation methods (repeatmodeler) that there are LTR, TIR and helitrons on this chromosome.
Thank you in advance,
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