CFM-ID Activity
Competitive Fragmentation Modeling for Metabolite Identification
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felicityallen
Activity for CFM-ID
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Pauline Lindholm created ticket #21
Error at CMakeLists.txt: 41 when trying to configure in cmake
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Felicity Allen modified a wiki page
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Lee Ferguson created ticket #20
"bad allocation" error in cfm-train
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Fix bug in previous commit.
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Compiling the Source Code on Linux
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Run CFM-ID in ubuntu
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Apologies for the delay looking into this, it should now be fixed.
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Updating to code to work with latest RDKit versions.
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I'm running into the same problem here with my installation on MacOS (High Sierra). RDKit version 2018.09.1 also seems to cause issues with the FindRDKit.cmake script. My RDBASE environment variable is correctly set, but I still can't get cmake to find the libraries. Has anyone solved this?
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David Skelton created ticket #19
Options for Features and Param Files
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missing test file
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kaushali de silva posted a comment on ticket #17
Check whether you correctly add RDBASE to your environment variable.
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This is spectrum file I am using.
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CFM-ID issue with candidate file
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Michael Stravs created ticket #17
Compatibility with RDKit 2017
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Many thanks to both of you for sharing these, I'll put a link back to this issue from the Wiki.
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Many thanks to both of you for sharing these, I'll add the file and put a link back to this issue from the Wiki.
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Try ./fraggraph-gen.exe (i.e. put a ./ in front) Or alternatively add the directory with the cfm executables to your path.
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Hi Anthony, Glad to hear you're finding CFM useful. Seems like it's not finding the file at all, could be a problem with relative paths, I suspect CFM may not understand these. Maybe try moving feature_config.txt into the directory you're running it from or giving the full path to the file. Another note, CFM-train is pretty slow, so you may want to use a compute cluster of some kind if you have a lot of molecules in your training set. Cheers, Felicity
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Run CFM-ID in ubuntu
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Anthony Mills created ticket #15
CFM-train error
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Greetings, Our lab also ran into some issues while compiling the source code on Linux. Attached here is a file containing the comments/issues and fixes created by the computer scientist (Wim Cardoen) who installed it on our University's Center for High Performance Computing clusters. At the end of the file he presents some tricks with chrpath that may be useful to others.
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Anand Patel created ticket #14
Compiling the Source Code on Linux
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CFM-ID released /cfm-id-2.4_win32.zip
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Adding utility program compute-stats for comput...
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-Always combine peaks with masses equal at 10 d...
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-Model param files relied on altered default fo...
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Uploading precomputed spectra for HMDB for both...
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--Adding supplementary information for EI paper...
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-Adding supplementary information for EI paper ...
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Random seed initialization
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Some Name created ticket #12
Parsing spectrum file headers
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-Added timeout code on fragmentation graph comp...
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Adding example for cfm-train
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Add extra warnings and abort training code if t...
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Tobias Kind created ticket #11
Thiophene fails
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-Uploading trained model for EI-MS (also restru...
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False arguments lead to extended run and crash
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Examples of molecules
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RDKIT canon exception
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Hi Tobias, The bug here is actually with the old version not the new. The input spectrum-molecule...
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Add cfm-train 2.0 example to WIKI
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Sorry this is actually a Milestone 2.0 issue.
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Add cfm-train example to WIKI
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cfm-id-2.0_win32 issue
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Another big apology for the long delay, I was hoping to have the branched code out...
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Another big apology for the long delay, I was hoping to have the branched code out...
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As per the other ticket: Apologies for the long delay - the latest version of CFM...
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Apologies for the long delay - the latest version of CFM (2.0) is able to process...
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CFM-2.0: Includes EI-MS support (including isot...
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negative_se_params.zip is corrupt
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James Jeffryes modified a comment on ticket #7
Thanks for the prompt reply! Indeed the error was on my end. I didn't realise when...
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Thanks for the prompt reply! Indeed the error was on my end. I didn't realise when...
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Hi James, Sorry to hear that. I've just double-checked and it works fine for me....
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negative_se_params.zip is corrupt
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Echoing Tobias, this error is thrown with any porphryn ring, includeing when the...
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-Adding molecule lists for negative data, hmdb ...
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-Adding molecule lists for negative data, hmdb ...
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command line args polishing
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WIKI fraggraph-gen example
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Done. Thanks!
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WIKI fraggraph-gen example
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