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stajichlab / OrthoMCL

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orthomclBlastParser error #10

Closed anu24s closed 3 years ago

anu24s commented 3 years ago

When I run orthomclBlastParser I get the error Illegal division by zero at orthomclBlastParser line 116.

Do you have any suggestion on how to solve this? Thanks in advance.

hyphaltip commented 3 years ago

I would not use this code -use the formal releases from the OrthoMCL team or use OrthoFinder2 as a more modern and appropriate tool.

Jason E Stajich, PhD Professor, Dept of Microbiology and Plant Pathology Chair, Academic Senate, Riverside Division University of California, Riverside

Fellow, CIFAR Fungal Kingdom: Threats and Opportunities https://www.cifar.ca/research/program/fungal-kingdom email: jason.stajich@ucr.edu twitter: @stajichlab http://twitter.com/stajichlab @hyphaltip http://twitter.com/hyphaltip @zygolife http://twitter.com/zygolife website: http://lab.stajich.org office: +1 951.827.2363 mobile: +1 909.333.6709

On Mon, Nov 16, 2020 at 12:40 PM anu24s notifications@github.com wrote:

When I run orthomclBlastParser I get the error Illegal division by zero at orthomclBlastParser line 116.

Do you have any suggestion on how to solve this? Thanks in advance.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stajichlab/OrthoMCL/issues/10, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5O54Q5KVSACILW5RSDTSQGE3PANCNFSM4TXVRTCQ .

anu24s commented 3 years ago

I am using customized version of OrthoMCL based on v2.0.9 and which is used within the OrthoMCL Pipeline. My OrthoMCL Pipeline run got stopped in between, so from " Re-run orthoMCL-pipeline from a given stage ? #27 " , I started running orthomclBlastParser script using my blast results obtained.

I am clueless what to be done. where can I find formal releases from the OrthoMCL script? Please help.

hyphaltip commented 3 years ago

please don't use this sqlite version and I would contact the main authors and their site is here https://orthomcl.org/common/downloads/software/ https://orthomcl.org/orthomcl/

Jason E Stajich, PhD Professor, Dept of Microbiology and Plant Pathology Chair, Academic Senate, Riverside Division University of California, Riverside

Fellow, CIFAR Fungal Kingdom: Threats and Opportunities https://www.cifar.ca/research/program/fungal-kingdom email: jason.stajich@ucr.edu twitter: @stajichlab http://twitter.com/stajichlab @hyphaltip http://twitter.com/hyphaltip @zygolife http://twitter.com/zygolife website: http://lab.stajich.org office: +1 951.827.2363 mobile: +1 909.333.6709

On Mon, Nov 16, 2020 at 1:00 PM anu24s notifications@github.com wrote:

I am using customized version of OrthoMCL http://orthomcl.org/common/downloads/software/v2.0/ based on v2.0.9 and which is used within the OrthoMCL Pipeline https://github.com/apetkau/orthomcl-pipeline. My OrthoMCL Pipeline run got stopped in between, so from " Re-run orthoMCL-pipeline from a given stage ? #27 " , I started running orthomclBlastParser script using my blast results obtained.

I am clueless what to be done. where can I find formal releases from the OrthoMCL script? Please help.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stajichlab/OrthoMCL/issues/10#issuecomment-728326438, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5OY7HN2WXMGPB4WC7ULSQGHGTANCNFSM4TXVRTCQ .

anu24s commented 3 years ago

Hi, I solved the error myself by concatenating all the blast outputs into a single file. It worked fine after that.