FragPipe v22 + DIA-NN 1.9 - Failed to generate skyline document

[emhumphries]

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Hi Fengchao, I'm trying to set up a DIA_SpecLib_Quant proteomic workflow using the latest versions of FragPipe and DIA-NN. The run finishes with DIA-NN output files however, I keep getting a skyline error that I can't seem to shake. I've tried Skyline 23.1 and Skyline daily 23.1.1.520 with no luck. I know the workflow was designed for DIA-NN 1.8.2 beta 27 so is the new version of FragPipe currently incompatible with DIA-NN 1.9? Regards, Erin

log_2024-06-14_12-25-07.txt [2024/06/13 17:36:39] Creating spectral library from files: [2024/06/13 17:36:39] library.tsv.skyline.speclib Process java.lang.ProcessBuilder@34f7cfd9 returned non zero value. Message: [2024/06/13 17:36:40] Error: ERROR: unable to determine DIA-NN report filename for 'library.tsv.skyline.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv)