2024-03-04

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2024.03.04

Todo today

Have a look at the COMMONS research discussion forum

- https://github.com/orgs/commons-research/discussions

Daily work on the Open Science for natural products research Viewpoint

See Viewpoint

Doing

Launching Sirius on Ola's dataset

Not sure what the duplicated feature id problem was again or where it came from. Relaunching the biostat tool box to double check.

Typical command would be

sirius -i tests/data/input_sirius.mgf --output tests/data/output_sirius --maxmz 800 config --IsotopeSettings.filter=true --FormulaSearchDB=BIO --Timeout.secondsPerTree=0 --FormulaSettings.enforced=HCNOP --Timeout.secondsPerInstance=0 --AdductSettings.detectable='[[M+H]+,[M-H4O2+H]+,[M+Na]+,[M+K]+,[M+H3N+H]+,[M-H2O+H]+]' --UseHeuristic.mzToUseHeuristicOnly=650 --AlgorithmProfile=orbitrap --IsotopeMs2Settings=IGNORE --MS2MassDeviation.allowedMassDeviation=5.0ppm --NumberOfCandidatesPerIon=1 --UseHeuristic.mzToUseHeuristic=300 --FormulaSettings.detectable=B,Cl,Br,Se,S --NumberOfCandidates=10 --ZodiacNumberOfConsideredCandidatesAt300Mz=10 --ZodiacRunInTwoSteps=true --ZodiacEdgeFilterThresholds.minLocalConnections=10 --ZodiacEdgeFilterThresholds.thresholdFilter=0.95 --ZodiacEpochs.burnInPeriod=2000 --ZodiacEpochs.numberOfMarkovChains=10 --ZodiacNumberOfConsideredCandidatesAt800Mz=50 --ZodiacEpochs.iterations=20000 --AdductSettings.enforced=, --AdductSettings.fallback='[[M+H]+,[M+Na]+,[M+K]+]' --FormulaResultThreshold=true --InjectElGordoCompounds=true --StructureSearchDB=BIO --RecomputeResults=false formula zodiac fingerprint structure canopus write-summaries

First we make sure to log via

sirius login --user-env SIRIUS_USERNAME --password-env SIRIUS_PASSWORD

sirius -i /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/mzmine/mapp_batch_00060_sirius.mgf --output /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/sirius/mapp_batch_00060 --maxmz 800 config --IsotopeSettings.filter=true --FormulaSearchDB=BIO --Timeout.secondsPerTree=0 --FormulaSettings.enforced=HCNOP --Timeout.secondsPerInstance=0 --AdductSettings.detectable=[[M+H3N+H]+,[M+Na]+,[M-H4O2+H]+,[M+K]+,[M-H2O+H]+,[M+H]+] --UseHeuristic.mzToUseHeuristicOnly=650 --AlgorithmProfile=orbitrap --IsotopeMs2Settings=IGNORE --MS2MassDeviation.allowedMassDeviation=5.0ppm --NumberOfCandidatesPerIon=1 --UseHeuristic.mzToUseHeuristic=300 --FormulaSettings.detectable=Cl,Br,S --NumberOfCandidates=10 --ZodiacNumberOfConsideredCandidatesAt300Mz=10 --ZodiacRunInTwoSteps=true --ZodiacEdgeFilterThresholds.minLocalConnections=10 --ZodiacEdgeFilterThresholds.thresholdFilter=0.95 --ZodiacEpochs.burnInPeriod=2000 --ZodiacEpochs.numberOfMarkovChains=10 --ZodiacNumberOfConsideredCandidatesAt800Mz=50 --ZodiacEpochs.iterations=20000 --AdductSettings.enforced=, --AdductSettings.fallback=[[M+Na]+,[M+K]+,[M-H2O+H]+,[M+H]+] --FormulaResultThreshold=true --InjectElGordoCompounds=true --StructureSearchDB=BIO --RecomputeResults=false formula zodiac fingerprint structure canopus write-summaries

Writing the command I realize that initially I might have sirius -i /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/mzmine, thereby specifying a whole directory instead of a file. This might be the source of the problem. I will relaunch the command with the correct input file. sirius -i /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/mzmine/mapp_batch_00060_sirius.mgf

I also realized another thing. The --RecomputeResults=false will only be effective if the input is changed to the previously computed directory. It seams obvious now that I think about it but since the commond doesnt throws an exception I didn't realize it. See https://github.com/boecker-lab/sirius/issues/69#issuecomment-1098053079

We had some awk commands which we cant find again.

Mooved to Awk

canopus_compound_summary.tsv > prefixed_canopus_compound_summary.tsv

awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $i = "canopus_" $i} {print}' canopus_compound_summary.tsv > prefixed_canopus_compound_summary.tsv

awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $i = "sirius_" $i} {print}' compound_identifications.tsv > prefixed_compound_identifications.tsv

awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $i = "dbresultsgnps" $i} {print}' e18c64bf354f457bb534c513821f7426.tsv > e18c64bf354f457bb534c513821f7426_prefixed.tsv

awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $i = "gnps_" $i} {print}' 0735059ee1034ad58a3861c2630e593f.tsv > 0735059ee1034ad58a3861c2630e593f_prefixed.tsv

awk -F'\t' 'BEGIN {OFS="\t"} NR==1 {for (i=1; i<=NF; i++) $i = "metannot_enhancer" $i} {print}' mapp_batch_00060_spectral_match_results_repond.tsv > mapp_batch_00060_spectral_match_results_repond_prefixed.tsv