Question: trinity error: possible unintended interpolation of @2 in string...
gravatar for chenzhuod
8 months ago by
chenzhuod30 wrote:

Hi, when I run trinity in local galaxy, it is error:

Fatal error: Exit code 2 ()
Possible unintended interpolation of @2 in string at 
/home/malab10/software/galaxy/database/dependencies/_conda/envs/__trinity@2.4.0/bin/Trinity line 43.

what can I solve it?

trinity memory galaxy local input • 531 views
ADD COMMENTlink modified 8 weeks ago by hsommer0 • written 8 months ago by chenzhuod30
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This error indicates that not enough memory was given to the job. However, sometimes input formatting problems can also produce this error (by triggering the job to use more memory than it really needs when processing correctly formatted data).

Start by checking how much memory has been given to the job. The requirements are the same as when the tool is used line-command, so the Trinity manual guidelines will apply.

Also check your inputs. How-to is explained in the Support FAQs:

For reference, Galaxy Administrator help can be found in these places:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
gravatar for hsommer
8 weeks ago by
hsommer0 wrote:

Trinity includes it's absolute installation path in the main perl script. It uses double quotes for that, which means that perl interprets the "@" contained in the path of the conda environment as a special character (used for string interpolation). To solve this, fix the script by either replacing the double quotes with single quotes or escape the "@" with a backslash.

ADD COMMENTlink written 8 weeks ago by hsommer0
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