no formula_candidate.tsv OR structure_candidate.csv

[zmahnoor14]

Hi SIRIUS team,

I have installed SIRIUS 5.6.3 CLI and GUI.

I cannot retrieve the proper output in the given output directory which was working fine with SIRIUS4.

To be sure I used the demo data Bicucullin.ms and ran both CLI and GUI separately. I saved the results from GUI in a directory. But I still dont receive the following three important files:

id/formula_candidate.tsv (id being the directory within the given output directory)
id/structure_candidate.tsv
canopus_summary.tsv

All the results appear fine in the GUI but I cannot retrieve above three files when I save the results as .sirius output. For CLI, I use the following command:
sirius --input Bicuculline.ms --output Bicuculline.json formula fingerprint structure --database coconut canopus

Do you know if I am using the right command to get results from sirius, csi:fingerid and canopus? Or is the output directory structure changed in SIRIUS5? If its has changed, how can I access the information from the above three files automatically (e.g: with fixed file names and a read-able format)?

Thanks : )

Kind regards,
Mahnoor

[mfleisch]

Hey Mahnoor,
the summaries can now be written independently from the computation by a separate subtool.
This allows to write them in different locations than the project data and easily rewrite them when needed.
In the GUI it is even possible to select a subset of the data to write summaries from.

You can just extend you command like this:
sirius --input Bicuculline.ms --output Bicuculline.json formula fingerprint structure --database coconut canopus write-summaries --output <OUTPUT_DIR>

If no output dir is given the summaties will be written to the project location (as in SIRIUS 4).

[zmahnoor14]

Hey Markus,

perfect thanks problem solved with write-summaries : )

Kind regards,
Mahnoor