ERROR No query file specified #446
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What does
ls -l hintsfile.gff
return? (I assume that this is the file that is reported with permission
denied, even though I am not really sure from the information given)
…On Thu, Dec 2, 2021 at 5:50 PM jonnyPizza ***@***.***> wrote:
braker.pl --cores 16 --gff3 --workingdir=$PWD"/" --species=XXX
--useexisting --genome=$FASTA --bam=Aligned.out.bam.sort
.../anaconda3/envs/evidencemodeler-1.1.1/opt/evidencemodeler
1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl augustus.hints.gff3 >
augustus.hints.evm_mod.gff3
*these are the lines of code I use involving braker and agustus, the
species tag is not one that is pre-existing but is added to the source
code.*
*the significant error lines are:*
...hintsfile.gff: Permission denied
.../anaconda3/envs/augustus-3.4.0/bin/augustus: ERROR No query file
specified. Type "augustus" for help.
*I have full permissions for braker and agustus, the same code worked when
a different species was inputted but, these errors keep popping up for this
one.*
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species/folder/folder/aug_hints_4: line 2: This is the full error code from that part. And it extends for each hints file created. |
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I can actually reproduce your problem. Working on finding out what is
happening there.
…On Thu, Dec 2, 2021 at 10:43 PM jonnyPizza ***@***.***> wrote:
species/folder/folder/aug_hints_4: line 2:
species/folder/folder/hintsfile.gff: Permission denied
This is the full error code from that part.
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I reproduced it with a genome that has semicolons in the scaffold names. Is
that the case for your genome as well?
Short term fix: remove the semicolons. But I am also working on a fix in
BRAKER. It's not an AUGUSTUS problem, it's in BRAKER.
On Fri, Dec 3, 2021 at 8:53 AM Katharina Hoff ***@***.***>
wrote:
… I can actually reproduce your problem. Working on finding out what is
happening there.
On Thu, Dec 2, 2021 at 10:43 PM jonnyPizza ***@***.***>
wrote:
> species/folder/folder/aug_hints_4: line 2:
> species/folder/folder/hintsfile.gff: Permission denied
>
> This is the full error code from that part.
>
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The issue has been addressed with commit Gaius-Augustus/Augustus@828bd2c in Augustus. This commit is not part of any release, yet (and that might take a long time), and thus it won't make it into conda installations for a while. You can manually replace the script createAugustusJobList.pl in your conda installation by https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/createAugustusJoblist.pl I hope this solves your problem. It won't if your issue was not caused by semicolons in fasta headers. |
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Error, cannot open file augustus.hints.gff3 at /modulefiles/anaconda3/envs/evidencemodeler-1.1.1/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl line 23. After correcting the fasta file for the semicolons, a new similar error appeared. |
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This looks like an evidence modeler problem... or was there another BRAKER
error message?
…On Thu, Dec 9, 2021 at 5:05 AM jonnyPizza ***@***.***> wrote:
Error, cannot open file augustus.hints.gff3 at
/modulefiles/anaconda3/envs/evidencemodeler-1.1.1/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl
line 23.
After correcting the fasta file for the semicolons, a new similar error
appeared.
Also I replaced the "createAugustusJoblist.pl" script.
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The semicolons remain problematic in fasta headers. We should implement a filter in braker.pl that warns users. |
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@LarsGab we should keep this in mind. |
braker.pl --cores 16 --gff3 --workingdir=$PWD"/" --species=XXX --useexisting --genome=$FASTA --bam=Aligned.out.bam.sort
.../anaconda3/envs/evidencemodeler-1.1.1/opt/evidencemodeler 1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl augustus.hints.gff3 > augustus.hints.evm_mod.gff3
these are the lines of code I use involving braker and agustus, the species tag is not one that is pre-existing but is added to the source code.
the significant error lines are:
...hintsfile.gff: Permission denied
.../anaconda3/envs/augustus-3.4.0/bin/augustus: ERROR No query file specified. Type "augustus" for help.
I have full permissions for braker and agustus, the same code worked when a different species was inputted but, these errors keep popping up for this one.
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