From rdemarco77 at gmail.com Thu May 12 15:08:04 2016 From: rdemarco77 at gmail.com (Ricardo de Marco) Date: Thu, 12 May 2016 10:08:04 -0300 Subject: [Inparanoid] problem runing InParanoid Message-ID: I am running inparanoid v4.1 and performed the installation of all components including v 2.2.16 of standalone blast. The last two runs I made with the program apparently performed well, but i got several warnings like this in the last steps of the program: no element found at line 1, column 0, byte -1 at ./blast_parser.pl line 110. [formatdb] WARNING: Cannot add sequence number 3 (lcl|3_./tmpd) because it has zero-length. [formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database. [blastall] WARNING: Unable to open tmpd.pin [blastall] WARNING: CDF34032: Unable to open tmpd.pin [blastall] WARNING: CDF34032: Unable to open tmpd.pin [blastall] FATAL ERROR: CDF34032: Database ./tmpd was not found or does not exist I would like to know if you know what could be causing this and if this affects the final result of the program. Thank you for your attention. Ricardo -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Tue May 24 16:17:12 2016 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 24 May 2016 16:17:12 +0200 Subject: [Inparanoid] problem runing InParanoid In-Reply-To: References: Message-ID: <57446268.7050201@scilifelab.se> sounds like you have zero-length sequences - try removing these. Erik On 2016-05-12 15:08, Ricardo de Marco wrote: > I am running inparanoid v4.1 and performed the installation of all > components including v 2.2.16 of standalone blast. The last two runs I > made with the program apparently performed well, but i got several > warnings like this in the last steps of the program: > no element found at line 1, column 0, byte -1 at ./blast_parser.pl > line 110. > [formatdb] WARNING: Cannot add sequence number 3 (lcl|3_./tmpd) > because it has zero-length. > > [formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST > database. > [blastall] WARNING: Unable to open tmpd.pin > [blastall] WARNING: CDF34032: Unable to open tmpd.pin > [blastall] WARNING: CDF34032: Unable to open tmpd.pin > [blastall] FATAL ERROR: CDF34032: Database ./tmpd was not found or > does not exist > I would like to know if you know what could be causing this and if > this affects the final result of the program. > Thank you for your attention. > Ricardo > > > _______________________________________________ > InParanoid-at-sbc.su.se mailing list > InParanoid-at-sbc.su.se at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From aoife.m.doherty at gmail.com Tue May 31 12:50:34 2016 From: aoife.m.doherty at gmail.com (aoife doherty) Date: Tue, 31 May 2016 11:50:34 +0100 Subject: [Inparanoid] c3 parameter in inparanoid.pl file Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sanae.el-mhijar at etu.univ-nantes.fr Tue May 31 14:23:19 2016 From: sanae.el-mhijar at etu.univ-nantes.fr (Sanae) Date: Tue, 31 May 2016 14:23:19 +0200 Subject: [Inparanoid] Error Message-ID: <574D8237.6000102@etu.univ-nantes.fr> Hello, I turn inparanoid on my data and i have thus error: Can't use an undefined value as an ARRAY reference at ./blast_parser.pl line 258, <> line 34. ... Done BLAST searches. Starting ortholog detection... Blast output file A->B is missing I dont understand this error, can you explain me please. Sanae