coordinates of repeats

[dgordon562]

Hey, Mark! You didn't bother to correct the coordinates of the repeats in the *.out file (probably because you didn't need them) . They are just in your split chunk coordinates--not in contig coordinates. If you (or anyone) needs those coordinates, I've corrected them in this fork of your pipeline:
https://github.com/hsiehphLab/RepeatMaskingChaisson

Best wishes,
David

[mchaisso]

Strange, I definitely have code to make the offset. Something must be off with what I checked in

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On Fri, Mar 29, 2024, 10:45 AM dgordon562 ***@***.***> wrote: Hey, Mark! You didn't bother to correct the coordinates of the repeats in the *.out file (probably because you didn't need them) . They are just in your split chunk coordinates--not in contig coordinates. If you (or anyone) needs those coordinates, I've corrected them in this fork of your pipeline: https://github.com/hsiehphLab/RepeatMaskingChaisson Best wishes, David — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKPGPSVKCC7A7QRBLEMMN3Y2WSFDAVCNFSM6AAAAABFOXDT6OVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIYTKNZWGMZDKNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dgordon562]

You corrected the coordinates in the masking, so the masked copy of the assembly is correct.

[mchaisso]

Hmm, I thought I also fixed the .out files -- I specifically recall checking them.

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On Fri, Mar 29, 2024 at 11:35 AM dgordon562 ***@***.***> wrote: You corrected the coordinates in the masking, so the masked copy of the assembly is correct. — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKPGPWLR3I7EG42WKVYK53Y2WX5XAVCNFSM6AAAAABFOXDT6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRXGU4DKOBVHA> . You are receiving this because you commented.Message ID: ***@***.***>

[mchaisso]

Ahh! I was hoping there was some config error on your end or that my code wasn't checked in. This is worst-case scenario since I need to rerun a bunch of jobs here. Thanks for the heads up!

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On Fri, Mar 29, 2024 at 11:49 AM Mark Chaisson ***@***.***> wrote: Hmm, I thought I also fixed the .out files -- I specifically recall checking them. On Fri, Mar 29, 2024 at 11:35 AM dgordon562 ***@***.***> wrote: > You corrected the coordinates in the masking, so the masked copy of the > assembly is correct. > > — > Reply to this email directly, view it on GitHub > <#1 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AAKPGPWLR3I7EG42WKVYK53Y2WX5XAVCNFSM6AAAAABFOXDT6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRXGU4DKOBVHA> > . > You are receiving this because you commented.Message ID: > ***@***.***> >

[dgordon562]

Happy to help!

[mchaisso]

Something changed in my code (perhaps I reverted accidentally to an older version) - the RepeatMasking I did for HPRC has the correct coordinates in the .out files. I'm really sorry to have sent you buggy code.

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On Fri, Mar 29, 2024 at 12:01 PM dgordon562 ***@***.***> wrote: Happy to help! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[mchaisso]

Can you submit a PR?

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On Fri, Mar 29, 2024 at 12:03 PM Mark Chaisson ***@***.***> wrote: Something changed in my code (perhaps I reverted accidentally to an older version) - the RepeatMasking I did for HPRC has the correct coordinates in the .out files. I'm really sorry to have sent you buggy code. On Fri, Mar 29, 2024 at 12:01 PM dgordon562 ***@***.***> wrote: > > Happy to help! > > — > Reply to this email directly, view it on GitHub, or unsubscribe. > You are receiving this because you commented.Message ID: ***@***.***>

[dgordon562]

Are you sure you want it? I made many, many changes for SLURM... each rule has something like this instead of "params": resources:
mem=8,
threads=8,
hrs=24

over the weeks, I think I've renamed some config parameters too...
you could clone my rep in a different directory and merge the snakemake with yours to choose the things you want. Sorry--it doesn't have just the changes you want.