Execute failed: Execution failed (exit code 127) in bowtie

KNIME Server
1

Hi Team,

we are trying to execute bowtie in the Knime aws server and getting Execute failed: Execution failed (exit code 127) in bowtie . when we checked in the server bowtie is working fine with permissions and privilege’s.
we are facing issue only from the knime web portal and server side it’s working fine.

Any help would be greatly appreciated.

Thanks in advance !

Regards,
Mukhendra

2

Hi All,

Please find the error msg in the below screen shot.

image
image691×262 7.72 KB

Regards,
Mukhendra

3

Hi @mukhendra,

We have little control over what an external tool does once it is called from KNIME. Based on your error, it seems like you were at least able to successfully connect to bowtie. Can you find out what exit code 127 is in bowtie? I’m not familiar with bowtie at all, so our ability to troubleshoot this is somewhat limited.

Apart from that, one thing you can also try is to use the External Tool (Labs) node (https://kni.me/n/vVYF69kf3S6GYyH2) instead of External Tool. See here for an example on how to use this node: https://hub.knime.com/knime/spaces/Examples/latest/06_Control_Structures/06_External_Applications/01_Example_for_the_external_tool_(Linux_or_Mac_only)

Cheers,
Roland

4

Hi Roland,

Thanks for the mail !

We are able to solve the issue with help of knime-support. we have been added the path of bowtie in Knime-editor.

After that restarted the services and it’s working fine.

Regards,
Mukhendra

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5

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