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ANGSD / angsd

Program for analysing NGS data.
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make -rf in realSFS #54

Closed ANGSD closed 7 years ago

ANGSD commented 7 years ago

This is not clearly defined. Should the analysis be done over each entry in the -rf file, or should a single estimate be obtained across the region spanned by the -rf

mlucenaperez commented 6 years ago

Hello there,

How did you solve this issue? I would like to run -rf using realSFS to have a single estimate across the regions. Did you implement that? I am having some issues trying to run realSFS fst stats on given regions. The file is not recognized even though I used it before with ANGSD.

`$NGSTOOLS/realSFS fst stats $POP1.$POP2.unfolded-lr.fst.idx -rf $REGIONFILE -> Assuming idxname:c_ll_ya_n008.x_ll_ba_n003.unfolded-lr.fst.idx -> Assuming .fst.gz file: c_ll_ya_n008.x_ll_ba_n003.unfolded-lr.fst.gz -> Problem opening file: '-rf'

head $REGIONFILE lp23.s00003:31499-31526 lp23.s00003:31532-31588 lp23.s00003:31595-31989 lp23.s00003:32018-32405 lp23.s00003:32614-32937 lp23.s00021:1901737-1901737 lp23.s00021:1901802-1901802`

Best,

María.

z0on commented 6 years ago

Looks like your $POP1.$POP2.unfolded-lr.fst.idx is not recognized as actual file name; try the same command without using $ variables? (Ie use actual file names)

Misha

iPhone. Autocorrections galore.

On Sep 5, 2018, at 4:24 AM, Maria Lucena Perez notifications@github.com wrote:

$POP1.$POP2.unfolded-lr.fst.idx

mlucenaperez commented 6 years ago

Thank you Misha, but I think that is not the issue. The command is working smoothly if I do not add -rf. Actually the "Assuming .fst.gz file: BLA" is right. The rf file that I am using has been previously used with other ANGSD command and works fine.

z0on commented 6 years ago

ah yes. It is just that your error message indicates that angsd thinks that “-rf” is not a switch but a file to be opened, suggests some mess-up in the command line to me…

On Sep 5, 2018, at 10:20 AM, Maria Lucena Perez notifications@github.com wrote:

Thank you Misha, but I think that is not the issue. The command is working smoothly if I do not add -rf. Actually the "Assuming .fst.gz file: BLA" is right. The rf file that I am using has been previously used with other ANGSD command and works fine.

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