OpenMS Tutorial: Missing file and mismatched files

[carobarry]

Hello,

I am unable to locate the smiles.csv file mentioned in the OpenMS (2.7.0) tutorial from the 'Digression: Working with chemical structures' section. So far I have been able of finding all the files mentioned in the OpenMS documentation from the Data archive (https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/). Is there a way for me to access the smiles.csv file?

Furthermore, when I attempted to find the iPRGlfq.consensusXML and experimentaldesign.csv files mentioned in the 'Conversion and downstream analysis' section of the tutorial, I only managed to locate the lfq.consensusXML and experimental_design.tsv from the data archive (https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/iPRG2015/). However, after running these in the recommended workflow (pictured in figure 19), I received the following error messages:

ERROR MSstatsConverter 6:3 Failing process stdout: [Error: Unexpected internal error (The filenames (extension ignored) in the consensusXML file are not the same as in the experimental design)]

ERROR MSstatsConverter 6:3 Failing process stderr: [/Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(290): The filenames (extension ignored) in the consensusXML file are not the same as in the experimental design, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(291): Spectra files (consensus map): , /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample1-A_0.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample1_B_1.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample1_C_2.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample2_A_3.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample2_B_4.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample2_C_5.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample3_A_6.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample3_B_7.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample3_C_8.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample4-A_9.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample4_B_10.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(294): JD_06232014_sample4_C_11.featureXML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(296): Spectra files (design): , /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample1-A.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample1_B.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample1_C.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample2_A.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample2_B.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample2_C.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample3_A.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample3_B.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample3_C.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample4-A.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample4_B.mzML, /Users/builder/jenkins/ws/openms/RC/openms_release_packaging/87227eb0/source/src/openms/source/FORMAT/MSstatsFile.cpp(299): JD_06232014_sample4_C.mzML]

Any feedback would be greatly appreciated!