problem with running PHLAWD

[nsa...@gmail.com]

Hi All,

I have just installed PHLAWD and ran the db update:

PHLAWD setupdb db.setup

that created the pln.db file

now, when I run the following: 

PHLAWD assemble config.PHLAWD

I am getting an error:

genbank database file: /groups/itay_mayrose/nivsabath/big.tree/pln.db # location of sqlite genbank database doesn't exist

even though I am specifying the exact path to the database (see config file below).

Any ideas how to make PHLAWD to work?

Thanks,

Niv

Config file:

clade = Fabaceae # should match an ncbi taxon name

search = rbcL # searches the descriptions, for multiple separate with spaces or commas

gene = rbcL2 # the directory and prefix to all output file names

mad = 0.01 # the threshold for breaking alignments, higher = less broken up

coverage = 0.7 # this is the stringency of the coverage for homology

identity = 0.5 # same as above but with identity

db = /groups/itay_mayrose/nivsabath/big.tree/pln.db # location of sqlite genbank database

knownfile = rbcL.keep # file with fasta sequences identifying gene region of interest

numthreads = 4 # number of threads for pthreads

Here are the location of the data base:

compute-7-0 23% pwd

/groups/itay_mayrose/nivsabath/big.tree

compute-7-0 24% ls -l | grep pln.db

-rwxrwxrwx 1 nivsabath lifesci1 14019650560 Oct 11 13:04 pln.db

[Stephen Smith]

Hm, This is very strange. Can you paste the whole output?

Are you running this on a cluster? Just wondering if there is something strange with the path or something like that.

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[nsa...@gmail.com]

Hi Stephen,

Thanks for the quick reply.

Yes, it's installed on a cluster and I am testing it on one node. Here is the path and output:

compute-7-0 2%  /share/apps/phlawd/bin/PHLAWD

PHLAWD 3.3a

you need more arguments.

usage: PHLAWD task configfile

possible tasks include:

        seqquery     -- just get the distribution of best hits to get cutoffs

        assemble     -- includes assembling and profiling

        justprofile  -- just profiles (assumes you have assembled)

        justassemble -- just assembles (assumes you will profile with justprofile

        setupdb      -- tasks performed on the SQLite database

        outlier      -- analyses on the detection of outliers

compute-7-0 3%

compute-7-0 3% /share/apps/phlawd/bin/PHLAWD assemble config.PHLAWD

genbank database file: /groups/itay_mayrose/nivsabath/big.tree/pln.db # location of sqlite genbank database doesn't exist

compute-7-0 4% PHLAWD assemble config.PHLAWD

genbank database file: /groups/itay_mayrose/nivsabath/big.tree/pln.db # location of sqlite genbank database doesn't exist

[Stephen Smith]

OK, i think it might be simply that you need to delete the # after your path to the db in the config file.

[nsa...@gmail.com]

Yes, it works now. Thanks!

it might be worth removing these comments from the example config file in 

http://phlawd.net/manual/quick-start-run

Cheers,

Niv

[Stephen Smith]

Good suggestion, I will fix that so they are on different lines