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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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halSnps Error: Segmentation fault #86

Open vsundaram opened 6 years ago

vsundaram commented 6 years ago

Hi,

I'm running halSnps on a hal alignment, and am getting the error: Segmentation fault.

I don't think this is a problem with hal-programs, because I've tested halStats on the alignment file, and that works.

Please let me know how to solve this issue. Thanks !

vsundaram commented 6 years ago

I have ensured that I'm using the names of the assemblies that is in the hal-file, and have also switched around with the order of the assembly names - nothing changes the error message.

I've also verified that my hal file is valid, using the halValidate program, and checked that other hal-programs works.

robsyme commented 6 years ago

What are the names of your assemblies? I ran into a similar problem when I had "." or "-" in my assembly names.

vsundaram commented 6 years ago

I'm using mouse strain data: there are no '.' and '-' in the assembly names. The issue was causing a crash that was then fixed at the beginning of December. Thanks !

On 19 January 2018 at 03:52, Robert Syme notifications@github.com wrote:

What are the names of your assemblies? I ran into a similar problem when I had "." or "-" in my assembly names.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/glennhickey/progressiveCactus/issues/86#issuecomment-358859626, or mute the thread https://github.com/notifications/unsubscribe-auth/AImu9-vfoTVb0UrzG9Kt4rxYhKn_IrzYks5tMBFugaJpZM4PilL4 .

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