output folder empty

[SaraManfredi]

Hello,

I'm running LipidMatch with my own data (positive) ddMS2, the folders: output, ddMS, Pos and PosByClass created are empty.

This is the error message at the end of the running code: "Read 103055 items Error in seq.default(16, nextSBlock - s_indicies[s] - 2, 2) : wrong sign in 'by' argument Called from: seq.default(16, nextSBlock - s_indicies[s] - 2, 2)"

Someone can help me?

Thank you in advance

[jeremykoelmel]

This is a common error were there are MS/MS scans with 1 or less fragments. If you remove these it should resolve your issue. Re-convert your files in MSConvert using the following parameters:

In the subset option (new MSConvert), under "Number of data points" put 2 in the first box, and nothing in the second. The following should be displayed: DefaultArrayLength | 2-

This will remove all MS/MS scans with 1 or less fragment which are causing the issue.

Let me know if this works. If not provide MSConvert parameters, vendor, and an example .ms2 data. As well as any new error messages.

[SaraManfredi]

I've used the MSConvert that come with ProteoWizard at this web site: (http://proteowizard.sourceforge.net/download.html) and used the following parameters:

peakPicking | vendor msLevel=2-2 threshold | absolute .0001 most-intense defaultArrayLength | 2-

The software don't convert the files: it's keep processing, but never complete the conversion.

Here an example of one of the files that i've use and converted previously (with only peakPicking and Threshold filters), the same that has caused the error:

08-05-19_ddMS2_pos.zip

[jeremykoelmel]

Please report this MSConvert related issue to: https://github.com/ProteoWizard/pwiz/issues

[jeremykoelmel]

Can you include solution here?

[SaraManfredi]

I've used the R and MSConverter version that come with LipidMatchflow