vcf2treemix.py output ===> input to Treemix

[Razi1026]

Hi,

I ran this:
python vcf2treemix.py -vcf file.vcf -pop poplist.txt

I got one output: "file.tmix"

head file.tmix
A B C D E F G
24,11 27,13 12,9 16,10 22,8 22,13 21,8
27,14 36,10 23,7 17,8 24,13 27,8 23,17

Now I am going to run treemix1.13 that need zip file and I simply zipped it:
gzip file.tmix ====> file.tmix.gz

then run treemix:
treemix -i input file.gz -o out

BUT, it doesn't work:

TreeMix v. 1.13
$Revision: 231 $
ERROR: input is not gzipped (only .gz files accepted)

I am not sure if this error is because of input or treemix error? (if I put wrong input name, again I get this error)

Would you please help me to run this? Thank you very much!

[StuntsPT]

Hi @Razi1026 ,
I did not develop the script you are using, but let me try to help.
To make sure the compression went well, try to issue the following command:

zcat file.tmix.gz | head

If the resulting output is equal to the contents of the original file, then the compression went well, otherwise you may have some error with gzip.
Also, are you sure you are issuing the correct filename to treemix in your command? In your example you are missing .tmix. You may wish to double-check that, and alternatively, use the full path to the input file.
Hope this helps,

Francisco

[Razi1026]

Hi @StuntsPT,

Thank you very much for your reply.

I checked the head of zipped file. Both was the same (before/after zip).

The commad which I ran is:
treemix -i input /path_to_file/file.tmix.gz -o out

again I got the same error:

TreeMix v. 1.13
$Revision: 231 $
ERROR: input is not gzipped (only .gz files accepted)

I have these outputs, but they are empty:

out.llik 
out.treeout.gz

I am not sure how can I solve this error!! I will be thankful if you have any idea to help. Thank you vey much.

I ran this and surprising, I didn't get error that: there is no input.
(I ran these both and got the same error about zip file!!!)

treemix -i input n.gz -o out  (here I don't have n.gz file)
treemix -i input 

[StuntsPT]

Ok, this is really wierd, and it is suggestive of an issue with your copy of treemix.
I'd recommend trying to use treemix with an example file that you are sure should work (if the original program does not have examples, try obtaining a working datafile from some paper that used it and made it available). You may also want to try different ways to install treemix (OS repository, conda, compile from source, etc...)

Best,
Francisco