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You may come across an error in CAFA where once you remove a particular sample from the working directory that doesn't have a ladder (as shown in the picture below), you keep coming across more samples that do not have a ladder. The error is in the sample directly after the sample that supposedly does not have a ladder. In this example, the error sample is the sample after TetCEOH2.B10; the TetMgDMS1.G09 sample. You should re-run CAFA with all the samples and determine which sample it is in the directory that directly after the no-ladder-sample. Once you have figured out the sample, remove it. You should find that no more other samples are coming up with no ladder once you have removed the error sample and re-run CAFA. If you have any questions regarding this problem, please feel free to email me, Kate, at ksimm004@umaryland.edu
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