Lumpyexpress does not run but do not appears error messages, why it can happen?

[Martaprf]

Hi! I am trying run lumpy express with the follow command: /home/mferreira/programs/lumpy-sv/bin/lumpyexpress -v \ -B sample.bam \ -S sample.splitters.sorted.bam \ -D sample.discordants.sorted.bam \ -o sample.vcf and I don´t get any error only this:
Sourcing executables from /home/mferreira/programs/lumpy-sv/bin/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)...

create temporary directory

Calculating insert distributions... Library read groups: id Library read length: 151 done 0

But looks that the lumpy do not start run and i do not understand why.

Someone can help with this issue?

Thanks a lot.

[ryanlayer]

Try using our new wrapper smoove https://github.com/brentp/smoove

On Tue, Apr 16, 2019 at 4:06 AM Martaprf notifications@github.com wrote:

Hi! I am trying run lumpy express with the follow command: /home/mferreira/programs/lumpy-sv/bin/lumpyexpress -v -B sample.bam -S sample.splitters.sorted.bam -D sample.discordants.sorted.bam -o sample.vcf and I don´t get any error only this: Sourcing executables from /home/mferreira/programs/lumpy-sv/bin/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)...

create temporary directory

Calculating insert distributions... Library read groups: id Library read length: 151 done 0

But looks that the lumpy do not start run and i do not understand why.

Someone can help with this issue?

Thanks a lot.

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[lgmgeo]

Hi, I have the same problem with lumpyexpress. It works with some WGS bam files but not with others. And I don't understand why... I'm using lumpy-sv_0.2.13 and python 2.7.6. Is there any bugfix to use to solve this bug?

Many thanks for any help you can provide me

[ryanlayer]

Try using our new wrapper smoove https://github.com/brentp/smoove

On Apr 23, 2019, at 7:29 AM, lgmgeo notifications@github.com wrote:

Hi, I have the same problem with lumpyexpress. It works with some WGS bam files but not with others. And I don't understand why... I'm using lumpy-sv_0.2.13 and python 2.7.6. Is there any bugfix to use to solve this bug?

Many thanks for any help you can provide me

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[lgmgeo]

Thank you for your quick answer! Please, where can we find a complete and up-to-date protocol to detect SV from WGS data with Lumpy/Smoove?

[lgmgeo]

Does it mean that Lumpy is not maintained anymore?

[ryanlayer]

It is. smoove uses lumpy.

On Tue, Apr 23, 2019 at 8:11 AM lgmgeo notifications@github.com wrote:

Does it mean that Lumpy is not maintained anymore?

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[lgmgeo]

Is there a bugfix planned to be added to lumpy concerning this bug?

[lgmgeo]

Or do you have any explanation about the cause?

[ryanlayer]

It’s petty hard for me to debug issues without data, commands, and details about the runtime environment.

On Apr 23, 2019, at 2:24 PM, lgmgeo notifications@github.com wrote:

Or do you have any explanation about the cause?

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[lgmgeo]

Sorry, never answered. Using smoove solved the problem. This issue can be closed.