[Inparanoid] c3 parameter in inparanoid.pl file

[aoife doherty]

Hi all, I'm really struggling to use this software and would appreciate
help.

The aim: I have a set of 20 mammalian species from a variety of sources
(i.e. are not all in the inparanoid database, thus I must do the command
line version of inparanoid to run blast and find orthologs). I want to
identify a set of one-to-one orthologs between all 20 species (i.e. the
"same" gene must be in all of the species).

I downloaded inparanoid version 4.1. I am trying to get the software to run
on the sample data sets provided, SC and EC.


First, I ran the software exactly as it was downloaded using the command:

perl inparanoid.pl EC SC


The error is:

200 sequences in file EC

200 sequences in file SC

Trying to run BLAST now - this may take several hours ... or days in worst
case!

Formatting BLAST databases

Done formatting

Starting BLAST searches...


Starting first BLAST pass for EC - EC on Tue May 31 11:29:04 BST 2016

sh: 1: blastp: not found


no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110



***


Then, I changed line 61 in the inparanoid.pl file from: "$blastall =
"blastp"; to "$blastall =
"/home/nis/home/1.PractisingInParanoid/inparanoid_4.1/ncbi-blast-2.3.0+/bin/blastp";"


where
"home/nis/home/1.PractisingInParanoid/inparanoid_4.1/ncbi-blast-2.3.0+/" is
where I've downloaded blast.


The error is this:

200 sequences in file EC

200 sequences in file SC

Trying to run BLAST now - this may take several hours ... or days in worst
case!

Formatting BLAST databases

Done formatting

Starting BLAST searches...


Starting first BLAST pass for EC - EC on Tue May 31 11:30:10 BST 2016

USAGE

  blastp [-h] [-help] [-import_search_strategy filename]

    [-export_search_strategy filename] [-task task_name] [-db database_name]

    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]

    [-negative_gilist filename] [-entrez_query entrez_query]

    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
(etc...more options that I have deleted for sake of space).



DESCRIPTION

   Protein-Protein BLAST 2.3.0+


Use '-help' to print detailed descriptions of command line arguments

========================================================================


Error: Unknown argument: "C3"

Error:  (CArgException::eInvalidArg) Unknown argument: "C3"


no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110


***

I need to fix the "Error: Unknown argument "C3".

1. I tried to find an older version of blast to run this command on, or to
run with legacy blast instead. I cannot find an older version of blast (and
this probably isn't a good idea anyway).

2. I tried to remove the "-C3" from the inparanoid.pl file on line 1765,
but then the script doesn't run as obviously this command is needed.

3. I've tried to find out what the -C3 filter did in the blast all program:
http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastall.html.


All of the files that I've used to try to get this to work are freely
available (i.e. I used the EC and SC sample files in inparanoid v 4.1, and
the only other external file that I used was ncbi-blast-2.3.0+ from the
ncbi website.

If someone could tell me what I can fix to make the sample files work, I
would appreciate it.

Thanks
Eva
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