I have tried to process multiple datasets using MetaboAnalyst’s Asari capabilities. I tried the “QuickDemo” dataset provided on the spectra processing landing page. I selected the dataset, then hit proceed. The only parameter I modified is selecting Asari. In all instances, the job appears to do nothing and I am prompted with “Please define your running plan…” message. You can refer to job ID 27989 as an example. I have faced similar issues using my own MS1 data (which I have used previously for the asari tutorials and it completes using Asari.app in less than 5 minutes) and the exposome test dataset similarly fails. I have tried both Firefox and Chrome after resetting both browsers to no avail.
Perhaps I simply need to wait longer, but as a developer on Asari and experienced user, I know that it should process the data pretty quickly so I don’t think that is the case. The text box never updates and the phrasing of the “Please define your running plan…” make it seem that there is something missing despite following the GUI. My collaborators have been having similar issues with the Asari integration so I do not believe it is an isolated problem.
Additionally, and I may be reading this incorrectly, the R code panel suggests that the cent-wave algorithm is still being used although Asari does not employ cent-wave at all. Could this be related to the issues?
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| 1. | mSet<-InitDataObjects(“spec”, “raw”, FALSE, 150) |
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| 2. | CentroidCheck(‘REPLACE_WITH_YOUR_SINGLE_FILE_PATH’) |
| 3. | SetPeakParam(Peak_method = “centWave”, mzdiff = 0.01,snthresh = 10.0,bw = 10.0,ppm = 5.0,min_peakwidth = 5.0,max_peakwidth = 30.0,noise = 1000.0,prefilter = 3.0,value_of_prefilter = 100.0,fwhm = 30.0,steps = 2.0,sigma = 12.74,profStep = 1.0,minFraction = 0.8,minSamples = 1.0,maxFeatures = 100.0,max = 10.0,extra = 1.0,span = 0.25,integrate = 1.0,RT_method = “loess”,polarity = “negative”,perc_fwhm = 0.6,mz_abs_iso = 0.005,max_charge = 2.0,max_iso = 2.0,corr_eic_th = 0.85,mz_abs_add = 0.001,adducts = “NULL”,rmConts = TRUE, BlankSub = FALSE) |
| 4. | library(OptiLCMS); metaboanalyst_env ← new.env(); setwd(‘/data/glassfish/projects/metaboanalyst/guest15285954733003590135tmp’); mSet ← InitDataObjects(‘spec’, ‘raw’, FALSE); mSet ← UpdateRawfiles(mSet,c(‘HC-AUP8B.mzML’,‘HC-9X47O.mzML’,‘HC-AMR37.mzML’,‘CD-9OS5Y.mzML’,‘CD-6KUCT.mzML’,‘CD-9WOBP.mzML’,‘QC_PREFB02.mzML’)); print(getwd());data_folder_Sample ← ‘upload/’; plotSettings1 ← SetPlotParam(Plot=TRUE, dpi = 150); mSet ← ImportRawMSData(path = data_folder_Sample, plotSettings = plotSettings1); OptiLCMS:::MessageOutput(’ Step 2/6: Start raw spectral processing with Asari! This step may take a long time…', ’ ', NULL) |