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zkutalik / ssimp_software

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Any idea what this error mean? #98

Open drveera opened 5 years ago

drveera commented 5 years ago
Screen Shot 2019-05-02 at 19 02 50

Hi I am trying to use the latest version. I have no issues with the old version 0.1, but the latest version is throwing this error. I couldn't understand the meaning of the error message. I'm happy to answer any further questions you'll have in relation to this error message. Thanks :) regards Veera

sinarueeger commented 5 years ago

Hi Veera, Could you provide us with the full error message, the exact command used, and the first few lines of the input files, so we can try to reproduce your error?

@zkutalik @aaron-mcdaid-zalando

MarioGuCBMR commented 4 years ago

Hi all,

I have found the same error. I have the latest version and I am using the linux compiled version. The commands are the following:

./ssimp --gwas gwas/small.random.txt --ref home/zlc436/reference_panels/1000genomes/ALL.chr{CHRM}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --out output.txt --sample.names /home/zlc436/reference_panels/1000genomes/integrated_call_samples_v3.20130502.ALL.panel/sample/super_pop=EUR

It seems that I could only download the 1000G data. Any other commands, with or without flags, shows me this error.

Thanks in advance for your help!

zkutalik commented 4 years ago

Hi Mario!

Could you please share the first couple of lines of your input file so that we can see the chr/pos in your small.random.txt summary stat file along with the exact error message? It seems your positions do not match any build...

Thanks!

MarioGuCBMR commented 4 years ago

Hi,

Thanks for your fast answer. Here you have it:

MarkerName Allele1 Allele2 Z rs5992801 T C 0.02625569846962102 rs1123031 T C 0.11867322079278599 rs5992111 T C 0.051311166629648186

It is the file I downloaded along with ssIMP. Also, I have tried to use Fasting Insulin summary statistics with the same header, but it does not work. I have seen the headers as A1 and A2 in some of your examples. Could it be that? I haven't tried it myself yet.

Cheers,

Mario

De: zkutalik [notifications@github.com] Enviado: jueves, 7 de mayo de 2020 9:44 Para: zkutalik/ssimp_software Cc: Mario García Ureña; Comment Asunto: Re: [zkutalik/ssimp_software] Any idea what this error mean? (#98)

Hi Mario!

Could you please share the first couple of lines of your input file so that we can see the chr/pos in your small.random.txt summary stat file along with the exact error message? It seems your positions do not match any build...

Thanks!

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zkutalik commented 4 years ago

Sorry, just to make sure, you got the exact same error message as drveera? Even iIdentical counts in each build category (0,47,14,0,899,237)?

MarioGuCBMR commented 4 years ago

That is a good question. I forward you here the error I get:

terminate called after throwing an instance of 'std::runtime_error' what(): locale::facet::_S_create_c_locale name not valid Aborted

My command is the following:

./ssimp --gwas gwas/small.random.txt --ref home/zlc436/reference_panels/1000genomes/ALL.chr{CHRM}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --out output.txt --sample.names /home/zlc436/reference_panels/1000genomes/integrated_call_samples_v3.20130502.ALL.panel/sample/super_pop=EUR

Cheers,

Mario

De: zkutalik [notifications@github.com] Enviado: viernes, 8 de mayo de 2020 9:56 Para: zkutalik/ssimp_software Cc: Mario García Ureña; Comment Asunto: Re: [zkutalik/ssimp_software] Any idea what this error mean? (#98)

Sorry, just to make sure, you got the exact same error message as drveera? Even iIdentical counts in each build category (0,47,14,0,899,237)?

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zkutalik commented 4 years ago

Could you please share the entire log file, just to see at what point this error occurred?

Thanks

Zoltan

zkutalik commented 4 years ago

Also could you please let me know what your computer gives if you type "locale"? Often "export LC_ALL=C" could solve this problem.

MarioGuCBMR commented 4 years ago

Hi,

When I run locale, I get the following:

LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL=

I guess the problem might be solved by rewriting it in the way you said it right?

Mario

De: zkutalik [notifications@github.com] Enviado: viernes, 8 de mayo de 2020 13:01 Para: zkutalik/ssimp_software Cc: Mario García Ureña; Comment Asunto: Re: [zkutalik/ssimp_software] Any idea what this error mean? (#98)

Also could you please let me know what your computer gives if you type "locale"? Often "export LC_ALL=C" could solve this problem.

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zkutalik commented 4 years ago

Yes, that command would be the first to try. Some others (https://github.com/potree/PotreeConverter/issues/281) suggest executing "export LC_ALL=C; unset LANGUAGE" before running our tool [or add these to your ".profile" file in your home directory to avoid typing it all the time].

This error has to do with your locale settings, in some cases it needs reinstallation of locale. (https://community.appdynamics.com/t5/Dynamic-Languages-Node-JS-Python/locale-facet-S-create-c-locale-name-not-valid/td-p/33693).

Please have a look around for other solutions in the internet.

MarioGuCBMR commented 4 years ago

Dear Zoltan,

Thank you so much, I think that with this I have a good grasp of the problem. Thank you again for you help and your quick answers.

Cheers,

Mario

De: zkutalik [notifications@github.com] Enviado: viernes, 8 de mayo de 2020 13:17 Para: zkutalik/ssimp_software Cc: Mario García Ureña; Comment Asunto: Re: [zkutalik/ssimp_software] Any idea what this error mean? (#98)

Yes, that command would be the first to try. Some others (potree/PotreeConverter#281https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpotree%2FPotreeConverter%2Fissues%2F281&data=02%7C01%7Cmario.garcia.urena%40sund.ku.dk%7C1941435f8c49410b420c08d7f34168f6%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637245334566548904&sdata=DuqybqIFQO4iamskMxq5baA3Ql77Tkj%2F4wZlD9Xga4Y%3D&reserved=0) suggest executing "export LC_ALL=C; unset LANGUAGE" before running our tool [or add these to your ".profile" file in your home directory to avoid typing it all the time].

This error has to do with your locale settings, in some cases it needs reinstallation of locale. (https://community.appdynamics.com/t5/Dynamic-Languages-Node-JS-Python/locale-facet-S-create-c-locale-name-not-valid/td-p/33693https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcommunity.appdynamics.com%2Ft5%2FDynamic-Languages-Node-JS-Python%2Flocale-facet-S-create-c-locale-name-not-valid%2Ftd-p%2F33693&data=02%7C01%7Cmario.garcia.urena%40sund.ku.dk%7C1941435f8c49410b420c08d7f34168f6%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637245334566548904&sdata=dCoU5J%2BeVBPslsCwCo8CY9hZPGgBb2YwtRdFK3XIpjA%3D&reserved=0).

Please have a look around for other solutions in the internet.

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zkutalik commented 4 years ago

Hope one of these suggestions will help sorting your problem! Please let us know if it still persists after trying all those tips.

Best

Zoltan