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chollenbeck / rad_haplotyper

MIT License
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Script runs but no output files #34

Closed baileyjc closed 4 years ago

baileyjc commented 4 years ago

Hello,

I tried running rad_haplotyper.pl on my data and it works but there are no output files.

Here is my code for running the script: rad_haplotyper.pl -v SNP.DP3g95p5maf05.HWE.recode.vcf -r reference.fasta -g SNP.recode.genepop -a SNP.recode.ima -p SNP.recode.popmap

These are the last two lines I get after all SNPs have been collapsed into haplotypes and everything is filtered: Writing Genepop file: SNP.recode.genepop No such file or directory at rad_haplotyper.pl line 946.

I checked line 946 which mentions a folder named POP, so I created a folder named POP and ran the code again but it still didn't create any output files.

Any help is appreciated! Thanks

sjoleary commented 4 years ago

Based on my experience, I suspect this has to do with rad_haplotyper not being able to find your popmap (from your line of code above -p SNP.recode.popmap). I've had this happen where I had a typo in my filename.

baileyjc commented 4 years ago

I have the popmap file in the same folder but isn't the "-p SNP.recode.popmap" naming the output files? My popmap file name is popmap.

pdimens commented 4 years ago

-p should be specifying your popmap file

baileyjc commented 4 years ago

Ah, well that solves it. My apologies but thank you for your time!