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AndersenLab / VCF-kit

VCF-kit: Assorted utilities for the variant call format
http://www.andersenlab.org
MIT License
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issue with primer3 #20

Closed amykwebster closed 5 years ago

amykwebster commented 5 years ago

I have installed VCF-kit and downloaded version WS245 of the C. elegans genome. I've also downloaded the VCF file from CeNDR. To generate primers that distinguish wild isolates based on SNPs, I've tried to run: vk primer snip --ref=WS245 WI.20180527.impute.vcf.gz

I get the following error output:

Using reference located at /Users/amy/.genome/WS245/WS245.fa.gz

--size ignored; Set to 600-800 bp.

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found Note: the --sample option not given, applying all records regardless of the genotype

Cannot find thermo path '/primer3_config/

I've checked that primer3 is installed, but I suspect there must still a problem with it. I've also tried uninstalling and re-installing primer3, but that doesn't seem to resolve the issue. Any insights on this issue would be appreciated! Thanks.

synmuv commented 5 years ago

Hi Amy, Did you get a reply from Dan? Thanks, Erik

On Wed, Nov 7, 2018 at 5:38 PM amykwebster notifications@github.com wrote:

I have installed VCF-kit and downloaded version WS245 of the C. elegans genome. I've also downloaded the VCF file from CeNDR. To generate primers that distinguish wild isolates based on SNPs, I've tried to run: vk primer snip --ref=WS245 WI.20180527.impute.vcf.gz

I get the following error output:

Using reference located at /Users/amy/.genome/WS245/WS245.fa.gz

--size ignored; Set to 600-800 bp.

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found Note: the --sample option not given, applying all records regardless of the genotype

Cannot find thermo path '/primer3_config/

I've checked that primer3 is installed, but I suspect there must still a problem with it. I've also tried uninstalling and re-installing primer3, but that doesn't seem to resolve the issue. Any insights on this issue would be appreciated! Thanks.

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amykwebster commented 5 years ago

Hi Erik,

I didn’t get a reply from Dan, but I did eventually figure out the problem. I used conda to manage my python environment, so the primer3_config path had to be changed in the primer3.py script (under thermo_paths) to where it was in my system, instead of the directory it would be put in through homebrew. It was a similar problem with “dyld: Library not loaded” error. I think I’ve got it working now! I can reply to the GitHub post with this info if it would be helpful.

Thanks, Amy

On Nov 23, 2018, at 9:51 AM, Erik Andersen notifications@github.com wrote:

Hi Amy, Did you get a reply from Dan? Thanks, Erik

On Wed, Nov 7, 2018 at 5:38 PM amykwebster notifications@github.com wrote:

I have installed VCF-kit and downloaded version WS245 of the C. elegans genome. I've also downloaded the VCF file from CeNDR. To generate primers that distinguish wild isolates based on SNPs, I've tried to run: vk primer snip --ref=WS245 WI.20180527.impute.vcf.gz

I get the following error output:

Using reference located at /Users/amy/.genome/WS245/WS245.fa.gz

--size ignored; Set to 600-800 bp.

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found Note: the --sample option not given, applying all records regardless of the genotype

Cannot find thermo path '/primer3_config/

I've checked that primer3 is installed, but I suspect there must still a problem with it. I've also tried uninstalling and re-installing primer3, but that doesn't seem to resolve the issue. Any insights on this issue would be appreciated! Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_AndersenLab_VCF-2Dkit_issues_20&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Gp9GcNUFSTEHtPoy51OSErch-TcP7EO8u9fdMSWzKDU&m=XO-CCKir8hX7bhmizdNsiCzH6iXgE4jARsjfdLGwNkI&s=PTyDPojqfN-1bzZiTUR9E4jnoKx03mfuVVZewkmp0ew&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AECPXQ-2DRyXexCRGIP4y-2DIZUCxuMwmyTnks5us2DPgaJpZM4YTooD&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Gp9GcNUFSTEHtPoy51OSErch-TcP7EO8u9fdMSWzKDU&m=XO-CCKir8hX7bhmizdNsiCzH6iXgE4jARsjfdLGwNkI&s=DnDKLil_3qWupfZNiVgvautSWLyWrI7adAWiCer95Oc&e= .

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danielecook commented 5 years ago

@amykwebster glad you were able to figure it out. Sorry I did not get back to you quick enough.

synmuv commented 5 years ago

Hi Amy, Great! I saw that Dan was working on the problem through GitHub as well. You could pull the update and see if it helps as well. I apologize for the delays. Best wishes, Erik

On Mon, Nov 26, 2018 at 10:50 AM amykwebster notifications@github.com wrote:

Hi Erik,

I didn’t get a reply from Dan, but I did eventually figure out the problem. I used conda to manage my python environment, so the primer3_config path had to be changed in the primer3.py script (under thermo_paths) to where it was in my system, instead of the directory it would be put in through homebrew. It was a similar problem with “dyld: Library not loaded” error. I think I’ve got it working now! I can reply to the GitHub post with this info if it would be helpful.

Thanks, Amy

On Nov 23, 2018, at 9:51 AM, Erik Andersen notifications@github.com wrote:

Hi Amy, Did you get a reply from Dan? Thanks, Erik

On Wed, Nov 7, 2018 at 5:38 PM amykwebster notifications@github.com wrote:

I have installed VCF-kit and downloaded version WS245 of the C. elegans genome. I've also downloaded the VCF file from CeNDR. To generate primers that distinguish wild isolates based on SNPs, I've tried to run: vk primer snip --ref=WS245 WI.20180527.impute.vcf.gz

I get the following error output:

Using reference located at /Users/amy/.genome/WS245/WS245.fa.gz

--size ignored; Set to 600-800 bp.

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/amy/anaconda/envs/py27/bin/samtools Reason: image not found Note: the --sample option not given, applying all records regardless of the genotype

Cannot find thermo path '/primer3_config/

I've checked that primer3 is installed, but I suspect there must still a problem with it. I've also tried uninstalling and re-installing primer3, but that doesn't seem to resolve the issue. Any insights on this issue would be appreciated! Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_AndersenLab_VCF-2Dkit_issues_20&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Gp9GcNUFSTEHtPoy51OSErch-TcP7EO8u9fdMSWzKDU&m=XO-CCKir8hX7bhmizdNsiCzH6iXgE4jARsjfdLGwNkI&s=PTyDPojqfN-1bzZiTUR9E4jnoKx03mfuVVZewkmp0ew&e= , or mute the thread < https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AECPXQ-2DRyXexCRGIP4y-2DIZUCxuMwmyTnks5us2DPgaJpZM4YTooD&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Gp9GcNUFSTEHtPoy51OSErch-TcP7EO8u9fdMSWzKDU&m=XO-CCKir8hX7bhmizdNsiCzH6iXgE4jARsjfdLGwNkI&s=DnDKLil_3qWupfZNiVgvautSWLyWrI7adAWiCer95Oc&e=

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-- Erik Andersen, Ph.D. Assistant Professor Department of Molecular Biosciences Northwestern University