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ANGSD / angsd

Program for analysing NGS data.
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Run restart + data conversion #521

Closed Imogen-D closed 2 years ago

Imogen-D commented 2 years ago

Hi,

I had a run of >500 RADseq samples that crashed due to running out of CPU hours (oops). However, my mafs and glf.pos files have finished writing to different chromosome numbers. I need a glf.gz file for downstream ngsrelate. Is there any way of A) restarting a run from the current end point or B) seeing which chromosome the glf.gz file (which is binary) is finished/written up to, so I can rerun (and then concatenate) the chromosomes that have not finished?

Also, is there any way of converting from the glf binary beagle to a 'normal' beagle file?

Many thanks!

isinaltinkaya commented 2 years ago

Hi,

You cannot restart the analysis from where it crashed. But you can split your analysis into chromosomes and merge it afterward. You can find a detailed tutorial for this at https://github.com/isinaltinkaya/angsd-troubleshooting-guide/blob/main/doGLF_chr-by-chr.MD

For outputting a beagle file please see http://www.popgen.dk/angsd/index.php/Glf_files.

Hope this helps, please feel free to reopen the issue if you have more questions about this.

Best, Isin

z0on commented 2 years ago

Hey - fun challenge! I would restart from scratch but on individual chromosomes (-r chr1 for example), run all those in parallel with -doGlf 2 to export straight to beagle. Then you can concatenate the beagle files (but tbh one chromosome is probably good enough for relatedness)

On Mon, Sep 19, 2022 at 6:07 PM Imogen Dumville @.***> wrote:

Hi,

I had a run of >500 RADseq samples that crashed due to running out of CPU hours (oops). However, my mafs and glf.pos files have finished writing to different chromosome numbers. I need a glf.gz file for downstream ngsrelate. Is there any way of A) restarting a run from the current end point or B) seeing which chromosome the glf.gz file (which is binary) is finished/written up to, so I can rerun (and then concatenate) the chromosomes that have not finished?

Also, is there any way of converting from the glf binary beagle to a 'normal' beagle file?

Many thanks!

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