Comments (6)
edgardomortiz
commented on August 25, 2024
Hi, what was the error exactly? If you write the path to the output folder with the option --output-folder the output files will be saved there. This is described in the README page.
Edgardo
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edgardomortiz
commented on August 25, 2024
Also keep in mind that the code was tested on Linux and Mac, from your description of a C drive I guess you are using Windows, it should work too but you have to be careful as to how you type the route to the output folder
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CHAOS324
commented on August 25, 2024
Thank you so much for replying. There's no error，actually the script runs well on Windows even if the VCF is as large as 1.7Tb.
I am a noob in bioinformatics and I don't even know how to use Linux! I just want to process a whole genome sequence VCF data to draw a tree.
My Python is installed in the C drive, my VCF and the vcf2phylip are in the D drive. I used the Windows cmd and used the -i function of vcf2phylip, and it worked, but it seems that freespace of my C drive is reducing as the script keeps running. So I guess the processed data is automatically output to the C drive. Because the remaining freespace of my C drive seems not enough to finish the convert, I wonder how to change the output path to my D drive, which should have enough freespace.
Sorry for my amateurish question and my poor expression. Thank you so so much for your answer.
Chaos
…---Original---
From: "Edgardo M. ***@***.***>
Date: Thu, Dec 29, 2022 22:24 PM
To: ***@***.***>;
Cc: ***@***.******@***.***>;
Subject: Re: [edgardomortiz/vcf2phylip] output path issue (Issue #40)
Also keep in mind that the code was tested on Linux and Mac, from your description of a C drive I guess you are using Windows, it should work too but you have to be careful as to how you type the route to the output folder
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edgardomortiz
commented on August 25, 2024
I understand, in your command add the path to the destination you want with the option --output-folder
Python commands can take multiple options (-i ,--output-folder, etc). Your command will have to be something like the following, where you have to replace path_to_my_D by the actual path in your computer (that can be something like D://myfiles/ but I'm not sure exactly because I haven't used Windows in a while...)
vcf2phylip.py -i myfile.vcf --output-folder path_to_my_D
Edgardo
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CHAOS324
commented on August 25, 2024
I got it. Again thanks for your help, it's a great encouragement for me to keep learning bioinformatics. : )
Chaos
…---Original---
From: "Edgardo M. ***@***.***>
Date: Sat, Dec 31, 2022 00:17 AM
To: ***@***.***>;
Cc: ***@***.******@***.***>;
Subject: Re: [edgardomortiz/vcf2phylip] output path issue (Issue #40)
I understand, in your command add the path to the destination you want with the option --output-folder
Python commands can take multiple options (-i ,--output-folder, etc). Your command will have to be something like the following, where you have to replace path_to_my_D by the actual path in your computer (that can be something like D://myfiles/ but I'm not sure exactly because I haven't used Windows in a while...)
vcf2phylip.py -i myfile.vcf --output-folder path_to_my_D
Edgardo
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Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: ***@***.***>
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edgardomortiz
commented on August 25, 2024
Glad to have helped!
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Related Issues (20)
- Hours taken to find the ploidy HOT 9
- Give option for name and directory of output file HOT 3
- Installation problem HOT 3
- transfer vcf file of SV into phylip failed HOT 5
- Invalid character * in the alignment HOT 10
- Coordinates of alignment sites HOT 2
- UnboundLocalError: local variable 'used_sites' referenced before assignment HOT 3
- Max character length for seq IDs HOT 2
- Deciding an outgroup to root the tree HOT 1
- error HOT 1
- ImportError: No module named pathlib HOT 2
- Can't regonized by Treebest to buid NJ tree
- All of the SNPs were removed by vcf2phylip HOT 3
- SNPs that passed the filters: 0 HOT 5
- All SNPs were removed by vcf2phylip HOT 3
- error: unexpected end-of-file. HOT 2
- unexpected token 'newline' error HOT 2
- KeyError: '2': always met this error when converting a vcf file to phylip file. HOT 5
- issues convert vcf file to phylyp HOT 9
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