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stajichlab / AAFTF

Automatic Assembly For The Fungi
MIT License
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AAFTF pipeline exiting when mito fails #26

Closed Kata-Pa closed 9 months ago

Kata-Pa commented 9 months ago

Hello,

Is it possible to run the AAFTF pipeline, skipping the mito step? I get an error from Novoplasty about invalid seed, which is not true, so it might be that no mitochondrial reads are present. Is there a way to make the pipeline ignore the mito step and continue with the rest?

Thank you in advance.

hyphaltip commented 9 months ago

No need to run that step unless you want the mt genome. Just run filter and assemble the steps are intended to be pick and choose

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On Thu, Feb 15, 2024 at 8:34 AM Kata-Pa @.***> wrote:

Hello,

Is it possible to run the AAFTF pipeline, skipping the mito step? I get an error from Novoplasty about invalid seed, which is not true, so it might be that no mitochondrial reads are present. Is there a way to make the pipeline ignore the mito step and continue with the rest?

Thank you in advance.

— Reply to this email directly, view it on GitHub https://github.com/stajichlab/AAFTF/issues/26, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5O6F6NGGLS4BG2FVP6LYTY2IRAVCNFSM6AAAAABDKSNYSGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEZTMOJXGAZTCMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Kata-Pa commented 9 months ago

Yes, of course this is an option, but instead of running each step separately, I was just wondering if the AAFTF pipeline command could be run directly with some parameter to skip one or more of the steps in between. In my case for example, I am interested in all the steps (1-9), except for the mito (step 2). If that is not possible and I want the whole pipeline, I have to run trim, filter and assemble but also vecscreen, rmdup, pilon, sort and assess. Do I interpret this right?

hyphaltip commented 9 months ago

sure it is always possible to develop another function or option to the pipeline all in one command but isn't my current use cases so I don't know when this will get attention right now. the whole point is you get to mix and match the steps you might run with the individual commands so you aren't bound to the "pipeline" command assumptions by any means.

here's an example of job script I use to run AAFTF that doesn't run mito https://github.com/stajichlab/KassonLab_Nectriaceae/blob/main/pipeline/asm/01_AAFTF.sh here's one for Mito https://github.com/stajichlab/KassonLab_Nectriaceae/blob/main/pipeline/asm/03_mito.sh

Jason E Stajich, PhD Professor and Vice-Chair, Dept of Microbiology and Plant Pathology University of California, Riverside

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On Thu, Feb 15, 2024 at 8:53 AM Kata-Pa @.***> wrote:

Yes, of course this is an option, but instead of running each step separately, I was just wondering if the AAFTF pipeline command could be run directly with some parameter to skip one or more of the steps in between. In my case for example, I am interested in all the steps (1-9), except for the mito (step 2). If that is not possible and I want the whole pipeline, I have to run trim, filter and assemble but also vecscreen, rmdup, pilon, sort and assess. Do I interpret this right?

— Reply to this email directly, view it on GitHub https://github.com/stajichlab/AAFTF/issues/26#issuecomment-1946575822, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5O3WNMXZ6CCWH7PPCU3YTY4RVAVCNFSM6AAAAABDKSNYSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBWGU3TKOBSGI . You are receiving this because you commented.Message ID: @.***>