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ANGSD / angsd

Program for analysing NGS data.
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-argument is unknown will exit #624

Closed MboiTui closed 5 months ago

MboiTui commented 5 months ago

Hello,

I am trying to produce an ancestral.fasta file to be used to build single population SFS.

I am encountering the error -argument is unknown will exit for two different arguments, depending on what version of angsd I am using.

When i use angsd 0.940-dirty, built in May 18 2023, with the below command:

angsd -b outgroup.list -out test -doCounts 1 -snp_pval 0.01 -doMaf 1 -doMajorMinor 1 -rmSNPs 1 -minInd 3 -explode 1 -gl 2

I get the error: -rmSNPs is unknown will exit

Thus i installed the ngsTools version of angsd (angsd version: 0.941-19-g2d1c533 (htslib: 1.18-4-g5098983e) build(May 27 2024 01:06:13).

Switching to this version and running the exact same command, I get the error:

-explode is unknown will exit

NOTE: i ran both of these interactively and retyped the command manually a number of time to ensure the error was not the result of hidden characters and/or formatting in the command.

Could you please suggest what I might be doing wrong?

Cheers, LVB

MboiTui commented 5 months ago

I was following the commands on the ANGSD website to produce the ancestral state fasta. Those did not include -doFasta. I have now added the -doFasta argument and the script is running well, thus I guess the issue was on my end.