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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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'-p' and '-E' parameters not working as expected #230

Open apcamargo opened 3 years ago

apcamargo commented 3 years ago

Expected Behavior

When I set the -pparameter to, for example 95, I expect that hits with probability lower than 95% would not appear in the output. The same happens to the -E parameter.

Current Behavior

Hits with probability lower than the one specified by -p are listed in the output file.

HH-suite Output (for bugs)

Query         orthogroup_msa_1
Match_columns 83
No_of_seqs    6 out of 8
Neff          1.58934
Searched_HMMs 100
Date          Tue Nov 10 07:33:10 2020
Command       /global/homes/a/acamargo/SCRATCH/.environments/comparative-genomics/bin/hhblits -cpu 64 -E 1E-5 -p 95 -M 50 -i proteins_aligned/orthogroup_msa.faa -d /global/cscratch1/sd/acamargo/Databases/UniRef30_2020_06_HH/UniRef30_2020_06 -o with_thresh.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 UniRef100_A0A0A9QVF6 Uncharact  85.8     2.4 5.4E-06   36.7   0.0   14   16-29     12-25  (160)
  2 UniRef100_A0A3A4WTT8 Uncharact  80.2     6.2 1.4E-05   33.3   0.0   20   49-68     43-62  (120)
  3 UniRef100_A0A0G4FQS2 Rubredoxi  78.1     5.1 1.8E-05   33.9   0.0   64    7-70     11-77  (160)
  4 UniRef100_UPI00142467B0 hypoth  76.2     9.9 2.2E-05   32.1   0.0   26   32-57      4-29  (118)
  5 UniRef100_A0A536LLW2 Y1_Tnp do  74.8      12 2.6E-05   32.0   0.0   25   46-70     74-98  (124)
  6 UniRef100_UPI00034A7219 hypoth  70.1      18   4E-05   34.0   0.0   32   40-71     27-58  (259)
  7 UniRef100_A1VUU2 Uncharacteriz  69.5      19 4.3E-05   32.4   0.0   23    5-27     54-76  (178)
  8 UniRef100_A0A4P9ZM92 Uncharact  68.4      21 4.7E-05   32.4   0.0   49    1-49      1-53  (186)
  9 UniRef100_A0A382KCK4 Uncharact  68.1      20 4.8E-05   31.1   0.0   19   60-78     46-64  (131)
 10 UniRef100_A0A3D4NVI0 Molecular  66.6      24 5.4E-05   26.6   0.0   32   43-74     15-48  (50)

Your Environment

HHblits 3.3.0 from Bioconda