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MS-DIAL / Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found
-> Make sure your files really contain only one run. There are instruments (like Sciex 6600) that overwrite files with the same name in case they are re-submitted (e.g., after an error or pause). Even if the original run did not contain any datapoints, there are two runs stored in one (for Sciex: wiff) file! You may not even notice because the file sizes only change marginally.
=> Solution: Conversion to mzML by MSConvert separates the runs. This means, however, that you have to convert all your files to mzML because MS-DIAL does not let you import files of different format (as far as I know).