It may take on average about 2-5 minutes to process one sequence on a node, what means that 10 nodes may be able to process no more than 3,000 - 5,000 sequences per day. The jobs are limited to 24hrs execution time, so if your job takes longer than that it will require restarting. You may want to split very big fasta files and submit them separately. Please contact us at biohpc@cac.cornell.edu if you need any help.

For more information about the original program please check the program's documentation.

Please acknowledge us in all publications and presentation of work that used our resources using the following text.

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Job name:   (please, no spaces, special characters etc., uderscore is OK)

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Query  file (Required):   uploadcopypaste

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Choose database for HMMER: Pfam_fs Pfam_ls     Output format:   CBSU HMMER raw

Run: Batch Real-time  nodes:    Cluster:     ( Show timeout info )

NOTE: P-HMMER currently uses nodes in exclusive mode so you select full nodes, not CPUs above.

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Options:

Cutoff E-value:  Initial timeout for one sequence (sec) keep timeout always equal initial timeout	Maximum Targets: Regular timeout for one sequence is  times average or maximum P-HMMER execution time
Extra HMMER options:

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