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mmseq convertalis will always have '^@' in the result

Open ekvbmipdn0811 opened this issue 2 months ago • 1 comments

When I using mmseq search uniref30, the result tsv always contain '^@' (also null) mmseqs version: 8cc5c

 search_param = ["--num-iterations", "3", "--db-load-mode", str(db_load_mode), "-a", "-e", "0.1", "--max-seqs", "10000", "--max-accept", "500"]
    if gpu:
        search_param += ["--gpu", str(gpu), "--prefilter-mode", "1"]
    if gpu_server:
        search_param += ["--gpu-server", str(gpu_server)]
run_mmseqs(mmseqs, ["search", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("tmp"), "--threads", str(threads)] + search_param)
format_param = ["--format-output", "query,target,evalue,bits,pident,alnlen,qcov,tcov,qstart,qend,tstart,tend,qlen,tlen,qaln,taln,cigar"]
convertalis_param = ["--db-load-mode", str(db_load_mode), "--db-output", "1"] + format_param
run_mmseqs(mmseqs, ["convertalis", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("uniref30_hits.tsv"), "--threads", str(threads)] + convertalis_param)
Image

So could you tell me whether it's the problem with the uniref30 s dataset or my use of mmseqs

ekvbmipdn0811 avatar Dec 03 '25 10:12 ekvbmipdn0811

another similar issue https://github.com/soedinglab/MMseqs2/issues/833

ekvbmipdn0811 avatar Dec 04 '25 07:12 ekvbmipdn0811