Error when running molecular docking

[jennaj]

Hi @Jeslyn_Jaic

Thanks for running that is a smaller simple history. Much easier to navigate!

@Jeslyn_Jaic

Then I used the vina tool and it seemed to work and there is an output, but its still highlighted as red overall even though each individual dataset is green.

The error is a bit harder to find – try clicking into the second output collection and you’ll see it. It seems to be a message about the final parsing step (the actual sdf was not an error).

Rerun

I would try a rerun first. Click into that single red dataset and use the rerun button. On the tool form, leave everything the same as the original run except toggle the “replace” option to Yes.

More details about how this works:

@jennaj

What to do

…
Later, if some fail, click into the collection and use the rerun icon (FAQ: Different dataset icons and their usage) on each failed dataset. This brings up the original tool form and you can run it again for just that single sample.

Bonus: If the failed job was run as part of a workflow, right above the Run Tool button (on the tool form) will be two new extra options. This is useful when running longer, complicated workflows, but also shorter ones. The result is indistinguishable from runs where everything worked perfectly to start with.

• Replace elements – this sorts the new output back into the original collection output nesting (with the already successful inputs).
• Resume dependencies – this starts up any downstream tools that were paused because of these upstream failures (assuming the new job works!)

Investigate

Then, if the job fails again, I would suggest reviewing the same way as we did the prior error. Compare the log content to what is in that specific chain of inputs to see if you can notice what is going wrong. Keep in mind that your job has two groups of inputs in a series.

The original dataset → then the sdf version that was created by the first step of the tool run → and finally this part of the tool that parsed the sdf output. By reviewing all together, and maybe comparing to the others in that group that were successful, you will probably be able to notice what went wrong.

I would also look at the formatting of that 10 ligand batch – especially if the error is the first or last in that set – to confirm the start and stop of that file are not missing any expected formatting. E.g. is not missing some header or is not truncated. (I hope this makes sense!).

Also keep in mind that parameters might be involved, and that single ligand was an edge case that needs to be managed. But I would always suggest looking a the data first before reviewing parameters!

Please give that a try and let us know what happens! If you get stuck and need more help, please post back screenshots of the relevant parts (to make sure we are looking at the same detail view) and we can work through this more. Try to keep the work in this same history for the single job rerun portion.

Let’s start there!