Report an error-Alignment input parse error:

[geng-lee]

I am using the protein sequence ".fasta"files of two species (oryza sativa HAK and Arabicdopsis thaliana KUP protein sequence ".fasta file") to create a new ".hmm" file with the following error： ocalhost:hmmer ligeng$ ./hmmbuild KUP.hmm AtKUP-OSHAK

hmmbuild :: profile HMM construction from multiple sequence alignments

HMMER 3.2.1 (June 2018); http://hmmer.org/

Copyright (C) 2018 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license.

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input alignment file: AtKUP-OSHAK

output HMM file: KUP.hmm

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idx name nseq alen mlen eff_nseq re/pos description

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Alignment input parse error: sequence sp|Q9FE38|POT3_ARATH has alen 775; expected 785 while reading aligned FASTA file AtKUP-OSHAK at or near line 30

How to solve this problem

[cryptogenomicon]

Please refer to the user guide. hmmbuild takes an alignment file as input, not an unaligned FASTA file. The error message indicates that it's trying to read your input as an aligned FASTA file and failing.