From nayaganviji at gmail.com Mon Feb 4 05:08:45 2013 From: nayaganviji at gmail.com (Vijay Kumar) Date: Mon, 4 Feb 2013 15:38:45 +0530 Subject: [Bio-Linux] help regarding BLAST running Message-ID: dear sir, i am Dr.VIJAY using BIOLINUX 7 for last 2 months.its really working good for biologist with own PC. now i face problem while working with BLAST run in terminal. when ever i run the BLAST i am getting error message like below for both single sequences and multiple sequences too. please help me( i am biology student, so i am not exposure to linux commend and error problem.THANK U SIR vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue 0.1 > vijay.blastx USAGE blastx [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-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] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-max_hsps_per_subject int_value] [-frame_shift_penalty frameshift] [-max_intron_length length] [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-query_gencode int_value] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version] DESCRIPTION Translated Query-Protein Subject BLAST 2.2.26+ Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: contig Error: (CArgException::eSynopsis) Application's initialization failed vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Simon.Wagstaff at liverpool.ac.uk Mon Feb 4 06:21:42 2013 From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon) Date: Mon, 4 Feb 2013 11:21:42 +0000 Subject: [Bio-Linux] help regarding BLAST running In-Reply-To: References: Message-ID: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> Dear Vijay, The problems are with your BLAST syntax. If you do a quick Google search you will find lots of web sites that will help you construct your BLAST search e.g. http://www.mathworks.co.uk/help/bioinfo/ref/blastlocal.html. You can also go to the NCBI documentation. Parameters you need are: -p program_name -d database_name -i input_sequence -e evalue (optional) -o output_file Looks me like you are searching nt query sequences against an nt database - if so blastx is also the wrong flavour of BLAST You need something like this blastall -p blastn -d my_database -i my_filename -e 0.1 -o my_output_file Avoid underscores in your filenames as they will be misinterpreted but BLAST as command-line arguments - see your error below. Simon From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Vijay Kumar Sent: 04 February 2013 10:09 To: bio-linux at nebclists.nerc.ac.uk Subject: [Bio-Linux] help regarding BLAST running dear sir, i am Dr.VIJAY using BIOLINUX 7 for last 2 months.its really working good for biologist with own PC. now i face problem while working with BLAST run in terminal. when ever i run the BLAST i am getting error message like below for both single sequences and multiple sequences too. please help me( i am biology student, so i am not exposure to linux commend and error problem.THANK U SIR vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue 0.1 > vijay.blastx USAGE blastx [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-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] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-max_hsps_per_subject int_value] [-frame_shift_penalty frameshift] [-max_intron_length length] [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-query_gencode int_value] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version] DESCRIPTION Translated Query-Protein Subject BLAST 2.2.26+ Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: contig Error: (CArgException::eSynopsis) Application's initialization failed vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Mon Feb 4 06:41:37 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Feb 2013 11:41:37 +0000 Subject: [Bio-Linux] help regarding BLAST running In-Reply-To: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> References: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> Message-ID: <1359978097.4567.342.camel@balisaur> Hi Simon and Vijay, I disagree with Simon - NR is a translated database so it is a peptide DB and blastx is therefore appropriate for a nucleotide query. Also, there is no reason to revert to the legacy "blastall" version of BLAST, even though it is still available on Bio-Linux 7. The only problem I can see is that your file name contains spaces. This is a bad idea as the shell has no way of knowing that the spaces are part of the file name and assumes they are new parameters to the command. In this case you can put the file name in "quotes" but a better idea is to ensure that your file names never contain spaces. Does that fix it? Cheers, TIM On Mon, 2013-02-04 at 11:21 +0000, Wagstaff, Simon wrote: > Dear Vijay, > > The problems are with your BLAST syntax. If you do a quick Google > search you will find lots of web sites that will help you construct > your BLAST search e.g. > http://www.mathworks.co.uk/help/bioinfo/ref/blastlocal.html. You can > also go to the NCBI documentation. > > > > Parameters you need are: > > > > -p program_name > > -d database_name > > -i input_sequence > > -e evalue (optional) > > -o output_file > > > > Looks me like you are searching nt query sequences against an nt > database - if so blastx is also the wrong flavour of BLAST > > > > You need something like this > > blastall -p blastn -d my_database -i my_filename -e 0.1 -o > my_output_file > > > > Avoid underscores in your filenames as they will be misinterpreted but > BLAST as command-line arguments - see your error below. > > > > Simon > > > > From: bio-linux-bounces at nebclists.nerc.ac.uk > [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Vijay > Kumar > Sent: 04 February 2013 10:09 > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] help regarding BLAST running > > > > > dear sir, > > > i am Dr.VIJAY using BIOLINUX 7 for last 2 months.its really working > good for biologist with own PC. now i face problem while working with > BLAST run in terminal. when ever i run the BLAST i am getting error > message like below for both single sequences and multiple sequences > too. please help me( i am biology student, so i am not exposure to > linux commend and error problem.THANK U SIR > > > > > > > > > vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] blastx -db > blastdb/nr.02 -query sra_data contig list - nucleotide_ > sequences.fasta -evalue 0.1 > vijay.blastx > > > USAGE > > > blastx [-h] [-help] [-import_search_strategy filename] > > > [-export_search_strategy filename] [-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] > > > [-subject subject_input_file] [-subject_loc range] [-query > input_file] > > > [-out output_file] [-evalue evalue] [-word_size int_value] > > > [-gapopen open_penalty] [-gapextend extend_penalty] > > > [-xdrop_ungap float_value] [-xdrop_gap float_value] > > > [-xdrop_gap_final float_value] [-searchsp int_value] > > > [-max_hsps_per_subject int_value] [-frame_shift_penalty > frameshift] > > > [-max_intron_length length] [-seg SEG_options] > > > [-soft_masking soft_masking] [-matrix matrix_name] > > > [-threshold float_value] [-culling_limit int_value] > > > [-best_hit_overhang float_value] [-best_hit_score_edge > float_value] > > > [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc > range] > > > [-strand strand] [-parse_deflines] [-query_gencode int_value] > > > [-outfmt format] [-show_gis] [-num_descriptions int_value] > > > [-num_alignments int_value] [-html] [-max_target_seqs > num_sequences] > > > [-num_threads int_value] [-remote] [-version] > > > > > > DESCRIPTION > > > Translated Query-Protein Subject BLAST 2.2.26+ > > > > > > Use '-help' to print detailed descriptions of command line arguments > > > ======================================================================== > > > Error: (CArgException::eSynopsis) Too many positional arguments (1), > the offending value: contig > > > Error: (CArgException::eSynopsis) Application's initialization failed > > > vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at ed.ac.uk Mon Feb 4 07:36:50 2013 From: tony.travis at ed.ac.uk (Tony Travis) Date: Mon, 04 Feb 2013 12:36:50 +0000 Subject: [Bio-Linux] help regarding BLAST running In-Reply-To: <1359978097.4567.342.camel@balisaur> References: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> <1359978097.4567.342.camel@balisaur> Message-ID: <510FAB62.3000202@ed.ac.uk> On 04/02/13 11:41, Tim Booth wrote: > Hi Simon and Vijay, > > I disagree with Simon - NR is a translated database so it is a peptide > DB and blastx is therefore appropriate for a nucleotide query. > > Also, there is no reason to revert to the legacy "blastall" version of > BLAST, even though it is still available on Bio-Linux 7. > > The only problem I can see is that your file name contains spaces. This > is a bad idea as the shell has no way of knowing that the spaces are > part of the file name and assumes they are new parameters to the > command. In this case you can put the file name in "quotes" but a > better idea is to ensure that your file names never contain spaces. > > Does that fix it? Hi, Tim. There is another potential problem because bio-linux-blast installs a profile.d fragment that sets the environment variable BLASTDB: > ajt at beluga:~$ cat /etc/profile.d/blast_environment.sh > #Added by package bio-linux-blast > export BLASTDB=/home/db/blastdb In Vijay's command-line he used: > blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue 0.1 > vijay.blastx So, he would be looking for: /home/db/blastdb/blastdb/nr.02 Unless he has created a directory called blastdb in the folder where he runs "blastall -p blastx" containing a 'formatted' BLAST database. It is also important to note that "bio-linux-blast" does NOT populate /home/db/blastdb with "nr", so Vijay will need to create the BLAST database using "formatdb" or copy the files from another machine. One other thing to note is that you need to set the Gnome Terminal to run as a login shell to source the correct files from /etc/profile.d and ~/.profile. The Gnome Terminal does not run as a login shell by default, because it is a sub-shell that only sources ~/.bashrc, and it doesn't inherit a shell login environment that a command-line sub-shell would. This is a known problem with Gnome Terminal "bash" sessions. > Gnome Terminal / Edit / Profile Preferences / Title and Command / Command [x] Run command as a login shell HTH, Tony. From tbooth at ceh.ac.uk Mon Feb 4 09:28:16 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Feb 2013 14:28:16 +0000 Subject: [Bio-Linux] help regarding BLAST running In-Reply-To: <510FAB62.3000202@ed.ac.uk> References: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> <1359978097.4567.342.camel@balisaur> <510FAB62.3000202@ed.ac.uk> Message-ID: <1359988096.4567.361.camel@balisaur> Hi Tony, > One other thing to note is that you need to set the Gnome Terminal to > run as a login shell to source the correct files from /etc/profile.d and > ~/.profile. The Gnome Terminal does not run as a login shell by default, > because it is a sub-shell that only sources ~/.bashrc, and it doesn't > inherit a shell login environment that a command-line sub-shell would. > This is a known problem with Gnome Terminal "bash" sessions. > > > Gnome Terminal / Edit / Profile Preferences / Title and Command / Command [x] Run command as a login shell I didn't know about this, but it won't affect most Bio-Linux users who will be in ZSH rather than BASH. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at ed.ac.uk Mon Feb 4 12:24:32 2013 From: tony.travis at ed.ac.uk (Tony Travis) Date: Mon, 04 Feb 2013 17:24:32 +0000 Subject: [Bio-Linux] help regarding BLAST running In-Reply-To: <1359988096.4567.361.camel@balisaur> References: <834710117A5F2048B9EC075D397DDB1B2449B83E@CHEXMBX1.livad.liv.ac.uk> <1359978097.4567.342.camel@balisaur> <510FAB62.3000202@ed.ac.uk> <1359988096.4567.361.camel@balisaur> Message-ID: <510FEED0.202@ed.ac.uk> On 04/02/13 14:28, Tim Booth wrote: > Hi Tony, > >> One other thing to note is that you need to set the Gnome Terminal to >> run as a login shell to source the correct files from /etc/profile.d and >> ~/.profile. The Gnome Terminal does not run as a login shell by default, >> because it is a sub-shell that only sources ~/.bashrc, and it doesn't >> inherit a shell login environment that a command-line sub-shell would. >> This is a known problem with Gnome Terminal "bash" sessions. >> >>> Gnome Terminal / Edit / Profile Preferences / Title and Command / Command [x] Run command as a login shell > > I didn't know about this, but it won't affect most Bio-Linux users who > will be in ZSH rather than BASH. Hi, Tim. I've just checked and found that exactly the same problem exists for "zsh". On a command-line login shell, these startup files are sourced: /etc/zsh/zshenv /etc/zsh/zprofile /etc/zsh/zshrc /etc/zsh/zlogin Invoking an interactive sub-shell from the login shell only sources: /etc/zsh/zshenv /etc/zsh/zshrc Setting Gnome Terminal to run "zsh" as a login shell sources: /etc/zsh/zshenv /etc/zsh/zprofile /etc/zsh/zshrc /etc/zsh/zlogin By default Gnome Terminal runs "zsh" as an interactive shell and only sources: /etc/zsh/zshenv /etc/zsh/zshrc HTH, Tony.