<div dir="ltr"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Hi all, I'm really struggling to use this software and would appreciate help.</font><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">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). </font></div><div><span style="background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif" color="#000000"><br></font></span></div><div><font color="#000000" face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)">I downloaded inparanoid version 4.1. I am trying to get the software to run on the sample data sets provided, SC and EC.</font></div><div><font color="#000000" face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)"><br></font></div><div><font color="#000000" face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)"><br></font></div><div><font color="#000000" face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)">First, I ran the software exactly as it was downloaded using the command: </font></div><div><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">perl <a href="http://inparanoid.pl">inparanoid.pl</a> EC SC</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">The error is:</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">200 sequences in file EC</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">200 sequences in file SC</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Trying to run BLAST now - this may take several hours ... or days in worst case!</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Formatting BLAST databases</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Done formatting</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Starting BLAST searches...</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Starting first BLAST pass for EC - EC on Tue May 31 11:29:04 BST 2016</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">sh: 1: blastp: not found</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal">
</p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">no element found at line 1, column 0, byte -1 at ./<a href="http://blast_parser.pl">blast_parser.pl</a> line 110</font></p><p style="margin:0px;line-height:normal"><br></p><p style="margin:0px;line-height:normal"><br></p><p style="margin:0px;line-height:normal">***</p><p style="margin:0px;line-height:normal"><br></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Then, I changed line 61 in the <a href="http://inparanoid.pl">inparanoid.pl</a> file from: "$blastall = "blastp"; to "$blastall = "/home/nis/home/1.PractisingInParanoid/inparanoid_4.1/ncbi-blast-2.3.0+/bin/blastp";"</font></p><p style="margin:0px;line-height:normal"><span style="background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif" color="#000000"><br></font></span></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">where "home/nis/home/1.PractisingInParanoid/inparanoid_4.1/ncbi-blast-2.3.0+/" is where I've downloaded blast.</font></p><p style="margin:0px;line-height:normal"><span style="background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif" color="#000000"><br></font></span></p><p style="margin:0px;line-height:normal"><span style="background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif" color="#000000">The error is this:</font></span></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">200 sequences in file EC</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">200 sequences in file SC</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Trying to run BLAST now - this may take several hours ... or days in worst case!</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Formatting BLAST databases</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Done formatting</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Starting BLAST searches...</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Starting first BLAST pass for EC - EC on Tue May 31 11:30:10 BST 2016</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">USAGE</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> blastp [-h] [-help] [-import_search_strategy filename]</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> [-export_search_strategy filename] [-task task_name] [-db database_name]</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> [-dbsize num_letters] [-gilist filename] [-seqidlist filename]</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> [-negative_gilist filename] [-entrez_query entrez_query]</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] (etc...more options that I have deleted for sake of space).</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">DESCRIPTION</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"> Protein-Protein BLAST 2.3.0+</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Use '-help' to print detailed descriptions of command line arguments</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">========================================================================</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Error: Unknown argument: "C3"</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">Error: (CArgException::eInvalidArg) Unknown argument: "C3"</font></p><p style="margin:0px;line-height:normal;min-height:13px"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></p><p style="margin:0px;line-height:normal">
</p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">no element found at line 1, column 0, byte -1 at ./<a href="http://blast_parser.pl">blast_parser.pl</a> line 110</font></p></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div>***</div><div><br></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">I need to fix the "Error: Unknown argument "C3".</font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">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).</font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">2. I tried to remove the "-C3" from the <a href="http://inparanoid.pl">inparanoid.pl</a> file on line 1765, but then the script doesn't run as obviously this command is needed. </font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000">3. I've tried to find out what the -C3 filter did in the blast all program: <a href="http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastall.html">http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/blastall.html</a>.</font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" style="background-color:rgb(255,255,255)" color="#000000"><br></font></div><div><font color="#000000" face="arial, helvetica, sans-serif">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 </font><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif">ncbi-blast-2.3.0+ from the ncbi website.</span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif">If someone could tell me what I can fix to make the sample files work, I would appreciate it.</span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif"><br></span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif">Thanks</span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif">Eva</span></div><div><span style="color:rgb(0,0,0);font-family:arial,helvetica,sans-serif"><br></span></div></div>