Invalid command line Unknown option wdb

[avr...@g.jct.ac.il]

after installing phylophlan on our  Unbuntu "12.04.4 LTS, Precise Pangolin we run the example from:

http://huttenhower.sph.harvard.edu/phylophlan

and downloading usearch, muscle,FastTree

on running the example provided in the above document, i get:

bioinfo:~/UNIX/nsegata-phylophlan-f2d78771d71d$ ./phylophlan.py -u example_corynebacteria --nproc 4

Extracting data/ppa.seeds.faa ... Done!

Extracting data/ppafull.aln.faa ... Done!

Extracting data/ppafull.xml ... Done!

Extracting data/ppafull.up2prots.txt ... Done!

Extracting data/ppafull.orgs2prots.txt ... Done!

Extracting data/ppaalns/ppa.aln.tar.bz2 ... Done!

Generating data/ppa.wdb (usearch indexed DB)... 

Invalid command line

Unknown option makewdb

Done!

Looking for PhyloPhlAn proteins in input faa files

Starting data/example_corynebacteria/C_accolens_ATCC49725.b6o...

Starting data/example_corynebacteria/C_ammoniagenes_DSM20306.b6o...

Starting data/example_corynebacteria/C_aurimucosum_ATCC700975.b6o...

Starting data/example_corynebacteria/C_efficiens_YS314A.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_genitalium_ATCC33030.b6o...

Invalid command line

Unknown option wdb

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_glucuronolyticum_ATCC51867.b6o...

Starting data/example_corynebacteria/C_glutamicum_ATCC13032K.b6o...

Invalid command line

Unknown option wdb

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_jeikeium_ATCC43734.b6o...

Starting data/example_corynebacteria/C_kroppenstedtii_DSM44385.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_matruchotii_ATCC14266.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_pseudogenitalium_ATCC33035.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_pseudotuberculosis_C231.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_pseudotuberculosis_I19.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_striatum_ATCC6940.b6o...

Invalid command line

Unknown option wdb

Starting data/example_corynebacteria/C_urealyticum_DSM7109.b6o...

Invalid command line

Unknown option wdb

Invalid command line

Starting data/example_corynebacteria/Streptomyces_outgroup1.b6o...

Unknown option wdb

Invalid command line

Unknown option wdb

Invalid command line

Unknown option wdb

Invalid command line

Unknown option wdb

All usearch runs performed!

Traceback (most recent call last):

  File "./phylophlan.py", line 792, in <module>

    faa2ppafaa( inps, pars['nproc'], projn )

  File "./phylophlan.py", line 291, in faa2ppafaa

    for l in open(dat_fol+i+".b6o").readlines()):

IOError: [Errno 2] No such file or directory: 'data/example_corynebacteria/C_accolens_ATCC49725.b6o'

bioinfo:~/UNIX/nsegata-phylophlan-f2d78771d71d$ ./phylophlan.py -u example_corynebacteria --nproc 4

[E] usearch not found or not in system path

Exiting... 

any pointers on how to debug this are greatly appreciated.

ihope i don't have to do source level debugging.

[Malte Rühlemann]

Hi,

you are probably running a usearch version higher than 5, which does not support wdb databases anymore. You should try to install usearch5 from the website and try again.

Best,

Malte

[Francesco Asnicar]

Hi,

the problem you mentioned is related to the version of usearch installed in your system.

The stable version of PhyloPhlAn requires usearch in the version 5.2.32.

Please check this page (https://bitbucket.org/nsegata/phylophlan/wiki/Home) at the section "External Software Dependencies" to make sure that the version of your software is the correct one.

Thanks,

Francesco Asnicar

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