Closed flaviode closed 4 years ago
MikkelSchubert
commented
4 years ago The error message you quoted does not exist in version 1.2.14, so I suspect that you are still running an old version of the pipeline. Can you try to running the BAM pipeline with the command-line option "--version"? That will print the exact version you are using.
And if the error message you are seeing now differs from what you copy/pasted before, then please include that as well.
flaviode
commented
4 years ago OPS!!I am sorry, It is 1.2.4…I will try to update the PALEOMIX version right now
Da: Mikkel Schubert Inviato: sabato 4 luglio 2020 12:58 A: MikkelSchubert/paleomix paleomix@noreply.github.com Cc: De Angelis, Flavio flavio.deangelis@yale.edu; Author author@noreply.github.com Oggetto: Re: [MikkelSchubert/paleomix] thank you, but this message appears with PALEOMIX v.1.2.14 too (#34)
The error message you quoted does not exist in version 1.2.14, so I suspect that you are still running an old version of the pipeline. Can you try to running the BAM pipeline with the command-line option "--version"? That will print the exact version you are using.
And if the error message you are seeing now differs from what you copy/pasted before, then please include that as well.
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MikkelSchubert
commented
4 years ago Closing due to lack of activity. Feel free to open a new issue if you still have this problem
Hi,
You appear to be using a version of PALEOMIX that is very, very old: The particular issue you are running into was fixed four years ago, and the version check was then completely removed two years ago because of related issues. So upgrading to a newer version of PALEOMIX (e.g. v1.2.14) should fix it. If it doesn't, then feel free to open another issue.
Best, Mikkel
Originally posted by @MikkelSchubert in https://github.com/MikkelSchubert/paleomix/issues/33#issuecomment-653735699
I repost the original message.
Hi, I run BAM pipeline but it returns:
Building BAM pipeline ...
Validating prefixes ... Running BAM pipeline ...
Checking file dependencies ...
Checking for required executables ...
Checking version requirements ...
Checking version of 'JAVA Runtime Environment' ... Program may be broken or a version not supported by the pipeline; please refer to the PALEOMIX documentation. Required: at least v1.6.x Search string: 'java version "(\d+)._' ---------------------- Command output ---------------------- openjdk version "1.8.0_252" OpenJDK Runtime Environment (build 1.8.0_252-8u252-b09-1~16.04-b09) OpenJDK 64-Bit Server VM (build 25.252-b09, mixed mode)
I guess this version is updated: how can I figure out this issue, without changing the openjdk version?
Thanks