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. Author manuscript; available in PMC: 2016 Nov 1.
Published in final edited form as: Nat Protoc. 2015 Oct 1;10(11):1643–1669. doi: 10.1038/nprot.2015.103

Table 7.

SuperFold Troubleshooting

Problem Possible cause Possible solution
Error message: “Program X not found in the path”. RNAstructure command-line tools not available to SuperFold. Make RNAstructure accessible by adding it to the shell path.
Error message: “DATAPATH not set…” RNAstructure DATAPATH is not set. Use the export command to set the variable DATAPATH to the location of the RNAstructure data tables (see hardware setup).
Error message: “Unexpected character in…”. Misformatted constraint file. Check the input files for extra spaces or special characters.
Error message: “pK region file incorrectly…”. Misformatted constraint file. Check pseudoknot constraint file for formatting. See the example file.
No base pairs are found in the partition function. Crash in the program partition gives empty output. Set the –partitionWindowSize flag to 1200 and rerun SuperFold. Depending on the sequence, a large SHAPE penalty can cause partition to malfunction with large window sizes.