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structure database search command line selecting 'all' databases: no fingerprints generated #92

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helenamrusso opened this issue Nov 3, 2022 · 1 comment
Closed

structure database search command line selecting 'all' databases: no fingerprints generated #92

helenamrusso opened this issue Nov 3, 2022 · 1 comment
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@mfleisch
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fixed v5.6.3 indicates that a bug or feature request has been fixed in v5.6.3

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@helenamrusso
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Hi,
I am using Sirius 5.6.1. in the command line, and I have been experiencing an issue with the structure database step. When I select to search in all, no fingerprints are generated. I can see that the files structure_candidates.tsv in each folder are generated by containing only the headers. As a result, no compound_identifications_adducts.tsv or compound_identifications.tsv is generated with the write-summaries command.

When I don't specify as 'all', it works correctly. If I specify it as PubChem, or a full list of all of the databases, it also works.
All the generated results, and the input sirius.mgf file can be found here: https://drive.google.com/file/d/1zhmSjBQPXegnsIEFUppIs7hOoyj_alDH/view?usp=sharing

Here are all the commands I ran for all the tests performed:

  • test_data_all: compound_identifications_adducts.tsv or compound_identifications.tsv; structure_candidates.tsv empty.
    /Users/helenarusso/Desktop/sirius_5_6_1.app/Contents/MacOS/sirius -i '/Users/helenarusso/Downloads/Test_data_Qemistree/sirius.mgf' -o '/Users/helenarusso/Downloads/Test_data_Qemistree/test_data_all' formula --profile orbitrap --database all --candidates 50 --ions-considered '[M+H]+' --tree-timeout 1600 --ppm-max 10 zodiac --thresholdFilter 0.98 fingerprint structure --database all canopus write-summaries

  • test_data_not_specified: all works correctly.
    /Users/helenarusso/Desktop/sirius_5_6_1.app/Contents/MacOS/sirius -i '/Users/helenarusso/Downloads/Test_data_Qemistree/sirius.mgf' -o '/Users/helenarusso/Downloads/Test_data_Qemistree/test_data_not_specified' formula --profile orbitrap --database all --candidates 50 --ions-considered '[M+H]+' --tree-timeout 1600 --ppm-max 10 zodiac --thresholdFilter 0.98 fingerprint structure canopus write-summaries

  • test_data_all_written: all works correctly.
    /Users/helenarusso/Desktop/sirius_5_6_1.app/Contents/MacOS/sirius -i '/Users/helenarusso/Downloads/Test_data_Qemistree/sirius.mgf' -o '/Users/helenarusso/Downloads/Test_data_Qemistree/test_data_all_written' formula --profile orbitrap --database all --candidates 50 --ions-considered '[M+H]+' --tree-timeout 1600 --ppm-max 10 zodiac --thresholdFilter 0.98 fingerprint structure --database BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE canopus write-summaries

  • test_data_pubchem: all works correctly.
    /Users/helenarusso/Desktop/sirius_5_6_1.app/Contents/MacOS/sirius -i '/Users/helenarusso/Downloads/Test_data_Qemistree/sirius.mgf' -o '/Users/helenarusso/Downloads/Test_data_Qemistree/test_data_pubchem' formula --profile orbitrap --database all --candidates 50 --ions-considered '[M+H]+' --tree-timeout 1600 --ppm-max 10 zodiac --thresholdFilter 0.98 fingerprint structure --database pubchem canopus write-summaries

I also take the opportunity to highlight that it seems there is a discrepancy in your structure --help description.
-d, --db, --database=[,...]
Search structure in the union of the given databases. If no
database is given 'ALL' internal databases are used.
Example: possible DBs: 'ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,
CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,
YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,
PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,
PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE'
Default: BIO

In the description it is mentioned that it should search in ALL, however, the default is BIO.

Thanks,
Helena
boeckergitlab pushed a commit to sirius-ms/sirius-libs that referenced this issue Jan 10, 2023
@mfleisch
fixed "all" database label bug in cli. fixes sirius-ms/sirius#92
1d300e1
@mfleisch mfleisch self-assigned this Jan 10, 2023
@mfleisch mfleisch added the fixed v5.6.3 indicates that a bug or feature request has been fixed in v5.6.3 label Jan 10, 2023
@mfleisch
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Hey @helenamrusso,
thanks for the detailed bug report. Both issues should be fixed in the upcoming release v5.6.3

mfleisch added a commit that referenced this issue Jan 10, 2023
@mfleisch
fixed "all" database label bug in cli. fixes #92
887c96d
mfleisch added a commit to sirius-ms/sirius-libs that referenced this issue Mar 3, 2023
@mfleisch
fixed "all" database label bug in cli. fixes sirius-ms/sirius#92
dec2962
mfleisch added a commit that referenced this issue Jun 27, 2023
@mfleisch
fixed "all" database label bug in cli. fixes #92
42fa093
mfleisch pushed a commit that referenced this issue Aug 2, 2024
remove .txt import, fixes #92
327ac8e
mfleisch pushed a commit that referenced this issue Aug 2, 2024
Merge branch '300-merge-sirius-libs-into-sirius-frontend-to-create-a-…
b2ff245 
…mono-repo' into 'master'

Resolve "Merge sirius-libs into sirius-frontend to create a mono repo."

Closes #300, #132, #126, #123, #128, #125, #127, #124, #122, #121, #120, #109, #115, #106, #99, #112, #111, #61, #110, #103, #108, #107, #104, #221, #102, #98, #198, #92, #94, #93, #85, #84, #87, #76, #56, #73, #32, #70, #65, #43, #63, #33, #53, #58, #59, #57, #54, #52, #41, #47, #50, #49, #48, #39, #46, #37, #38, #27, #34, #22, #31, #28, #18, #23, #21, #19, #9, #240, #280, #254, #242, #246, #238, #156, #25, #155, #189, #172, #154, #11, #6, #16, and #4

See merge request bright-giant/sirius/sirius-frontend!106
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