plink 1.9 --homozyg options error

[Nathalie Smogeli]

Hello, i am trying to get some ROH from my data and first i haf written all options into my scripts even though i decided to use default values. I get the error of where it says <parameter> only accepts 1 parameter. This confuses me very much because i think i have given it one parameter and that it states so before giving me the error. Now i have kept only the parameters im changing and it looks like this:

[Nathalie Smogeli]

heres the code for this particular section if it helps:

[Nathalie Smogeli]

ohno, i see i forgot that plink 1.9 may not accept pfiles. so I will have to change them all to bfiles or something else it will accept. Could that be whats causing this error?

[Nathalie Smogeli]

even if i run it with --vcf files then I get same error

[Christopher Chang]

There are MANY differences between your "code for this particular section" screenshot and the screenshot before that; the main thing in common between them is that both have (different!) mistakes that are UNRELATED to --homozyg-gap.

I cannot help you until you post a .log file describing a specific command that is failing, along with all the input files for that command, so I can reproduce on my end.  While what you've posted is better than nothing, in this case it's still too imprecise.

[Nathalie Smogeli]

The code and outfile when dropping other parameters

When i drop "group verbose and extend" also I get the error

Are there still mistakes besides the gap that need changing or what is going on?

[Christopher Chang]

Still can't help you, I can't reproduce what you're seeing.  I asked for ACTUAL INPUT FILES, not screenshots.

[Christopher Chang]

(including a literal .log file, because something funny may be going on with invisible characters)

[Christopher Chang]

Looking at the .out file, there are in fact extra spaces after "--homozyg-gap 10" in the log.  So I'm guessing that you have spaces after the backslash on the "--homozyg-gap 10" line of your script, and if you get rid of them you will no longer see this error message.

On Tuesday, November 21, 2023 at 12:02:08 AM UTC-8 nathalieal...@gmail.com wrote:

my input files are too big to post here, but I have tried uploading to disk and share the link here.

does this work?

https://drive.google.com/file/d/1cirSTJv4_ZE0cOkEk49rhl7V5fa3epn8/view?usp=sharing

https://drive.google.com/file/d/1LjBKf2xsIzeE7GQf-mMq2kN2KxLLl9Gd/view?usp=sharing

https://drive.google.com/file/d/1z0eS_zQDP2yCWLbO8EWtVghkA1D6pb7q/view?usp=sharing

[Nathalie Smogeli]

yup, that was it. The one braincell left was not functioning. I apologize for that!