pfam_scan.pl can't find the pfamdb
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3.5 years ago
MAPK ★ 1.9k

I am trying to run pfam_scan.pl script which keep generating this error below though both Pfam-A.hmm and Pfam-A.hmm.dat files are in /pfamdb. Can someone please help me identify the errors and resolve this?

perl /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/PfamScan/pfam_scan.pl -fasta Hannuus_494_r1.2.protein.fa -dir /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/database/pfamdb

 FATAL: can't find "Pfam-A.hmm" and/or "Pfam-A.hmm" binaries and/or "Pfam-A.hmm.dat" file in "/media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/database/pfamdb" at /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/PfamScan/pfam_scan.pl line 68.
pfamdb • 2.0k views
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3.5 years ago
h.mon 33k

You have to prepare the HMM database using HMMER3:

hmmpress Pfam-A.hmm
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Thank you !!

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