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iTAK
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Error: Sequence file ./Trinity.fasta_temp/protein_seq.fa is empty or misformatted #4

Open bioramg opened 1 year ago

bioramg commented 1 year ago

Hi, I try to analyze transcription factors and kinase family-related genes using the transcriptome data. I have the unigenes file in the fasta format. I am getting an error like this.

Error: Sequence file ./Trinity.fasta_temp/protein_seq.fa is empty or misformatted

[ERR]cmd: /home/raman/bin/iTAK/bin/hmmscan --acc --notextw --cpu 20 -o ./Trinity.fasta_temp/protein_seq.pfam.hmmscan.txt /home/raman/bin/iTAK/database/Tfam_domain.hmm ./Trinity.fasta_temp/protein_seq.fa

How to solve this issue.

I am looking forward to hearing from you.

With best regards, Raman. G

kentnf commented 4 months ago

please use the below command to check the input sequence file is not empty: seqtk seq -a ./Trinity.fasta_temp/protein_seq.fa | grep -c "^>"