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soedinglab / hh-suite

Remote protein homology detection suite.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
GNU General Public License v3.0
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addss.pl errors #247

Closed ksteczk closed 3 years ago

ksteczk commented 3 years ago

Hello, I have a little database for which I computed profiles and want to add a predicted secondary structure. I run the following command:

ffindex_apply db_wo_ss.ff{data,index} -i db.ffindex -d db.ffdata -- addss.pl -v 0 stdin stdout and get an error

ERROR in fork() A01.001_MER0000885: No such file or directory A01.001_MER0000885: No such file or directory

The identifier is in the index file:

A01.001_MER0000885 203883305 874969

and also is in the data file:

^@>A01.001_MER0000885 - pepsin A (Homo sapiens) #A01A#{peptidase unit: 63-388}~source PEPA_HUMAN~ VDEQPLENYLDMEYFGTIGIGTPAQDFTVVFDTGSSNLWVPSVYCSSLACTNHNRFNPEDSSTYQSTSETVSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISSSGATPVFDNIWNQGLVSQDLFSVYLSADDQSGSVVIFGGIDSSYYTGSLNWVPVTVEGYWQITVDSITMNGEAIACAEGCQAIVDTGTSLLTGPTSPIANIQSDIGASENSDGDMVVSCSAISSLPDIVFTINGVQYPVPPSAYILQSEGSCISGFQGMNLPTESGELWILGDVFIRQYFTVFDRANNQVGLAPVA >UniRef100_A0A3Q4MVP9 Peptidase A1 domain-containing protein n=1 Tax=Neolamprologus brichardi TaxID=32507 RepID=A0A3Q4MVP9_NEOBR --------------------------------IMKLAFAVFPMVALSECLVQIPLEKGKSAWEVLQEQGLWEEYRQKYPYNPMAKFDrSFAVGPESLTNDaglsYYGvISIGTPPQSFKVIFDTGSSNLWVPSIYCNSAactdkcncsaftahcgviqlnSSIYKQMFHELswlisVTCTDSICLcttqsealLFCNNNQRGSEVTFGGVDTNHYSGSITWIPLSNELYCQITVGSVCGNGQAVACNDGCQAIVDTGTSMIVGPQSDIDNINAWLGASS-QNGEYIVNCNNIGQMPDVTFNINGNQFTLPMCIS----S--CITGFSAT-----GGNMWTLGDVFLRQYYSIYNRGQNMLGLAKAR

Where the problem might be? The database was generated from fasta file with ffindex_from_fasta and then profiles were computed using hhblits_omp without errors.

ksteczk commented 3 years ago

Solved the issue. I didn't have addss.pl in my path. Stupid mistake. Sorry for bothering you.