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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Unknown option: threads #827

Closed Arodiansyah21 closed 1 month ago

Arodiansyah21 commented 1 month ago

Hey there,

I attempted to execute Braker using the following script:

home/achmad/Apps/BRAKER/BRAKER/scripts/braker.pl --genome=final_sequence.fasta --prot_seq=reference/protein_brakerdb.fasta --softmasking --workingdir=gene_prediction/braker --threads 100

However, it failed with an error message stating:

Unknown option: threads Error in command line arguments

Previously, the script ran successfully without the --threads argument, but it took a considerable amount of time to complete. I'm dealing with a large genome of Salacca zalacca.

I've already installed the "threads" Perl module.

Can anyone assist me with this issue?

Thank you.

KatharinaHoff commented 1 month ago

Are you using the latest version? An older version would not know this option.

Arodiansyah21 @.***> schrieb am Do. 16. Mai 2024 um 10:00:

Hey there,

I attempted to execute Braker using the following script:

home/achmad/Apps/BRAKER/BRAKER/scripts/braker.pl --genome=final_sequence.fasta --prot_seq=reference/protein_brakerdb.fasta --softmasking --workingdir=gene_prediction/braker --threads 100

However, it failed with an error message stating:

Unknown option: threads Error in command line arguments

Previously, the script ran successfully without the --threads argument, but it took a considerable amount of time to complete. I'm dealing with a large genome of Salacca zalacca.

I've already installed the "threads" Perl module.

Can anyone assist me with this issue?

Thank you.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/827, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JAOCB7JVSOGAIYFMM3ZCRRQPAVCNFSM6AAAAABHZVE6OWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4TSNRVGAZDMMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Arodiansyah21 commented 1 month ago

Hy Katharina,

We're currently utilizing Braker version 2.1.6. Furthermore, do you have guidelines on how to upgrade Braker to the latest version?

I'm worried that if I update to the latest version, our current Braker might not be usable, because I'm still a newbie in this field.

Thank you,

Arodiansyah21 commented 1 month ago

Hy Katharina,

We're currently utilizing Braker version 2.1.6. Furthermore, do you have guidelines on how to upgrade Braker to the latest version?

I'm worried that if I update to the latest version, our current Braker might not be usable, because I'm still a newbie in this field.

Thank you,

In my braker version. the output without "--threads" argument resulted like this

#CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: blaablaaablaaa............

So its consume a lot of times haha. Meanwhile, my computer having 112 CPU.

KatharinaHoff commented 1 month ago

If you use an older version, you have to use the older usage.

I generally recommend upgrading because a lot issues have been improved, accuracy has increased. But you are correct, some older features are not supported, anymore.

On Thu, May 16, 2024 at 12:59 PM Arodiansyah21 @.***> wrote:

Hy Katharina,

We're currently utilizing Braker version 2.1.6. Furthermore, do you have guidelines on how to upgrade Braker to the latest version?

I'm worried that if I update to the latest version, our current Braker might not be usable, because I'm still a newbie in this field.

Thank you,

In my braker version. the output without "--threads" argument resulted like this

#CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: blaablaaablaaa............

So its consume a lot of times haha. Meanwhile, my computer having 112 CPU.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/827#issuecomment-2114906965, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JAD6W7WHA2FUEXOE4DZCSGR7AVCNFSM6AAAAABHZVE6OWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJUHEYDMOJWGU . You are receiving this because you commented.Message ID: @.***>