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Hi! I tried the pipeline on the protein sequences of Arabidopsis and encountered an error. Could you please help me with this issue? Many thanks!
The all_PPR.hmm file was obtained from https://doi.org/10.5061/dryad.vdncjsxqf.
hmmsearch --domtblout Arabidopsis.domt --noali -E 0.1 all_PPR.hmm Arabidopsis.pep
java -jar ./OneKP-master/OneKP.jar Arabidopsis.pep Arabidopsis.domt
reading Arabidopsis.domt
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.substring(String.java:1967)
at pprfinder.PPRfinder.main(PPRfinder.java:62)
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
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