Closed sa256 closed 4 years ago
please edit the configuration file ncbiBlastConfig2-2-29.txt to change the location of blast, to match the location on YOUR system (eg. program:XXYOUR-BLAST-LOCATIONXX
Thanks for such a quick response! I followed the instructions and I could resolve it by using ncbiBlastConfig2-2-22.txt file with blastall instead of blastn (as there was no blastn in my bin directory). Hope this is fine.
But now I am facing another problem with same step (parseXMLblast.pl script). Now when I run it it gives me following error:
Bio::SearchIO: blastxml cannot be found
Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate Bio/SearchIO/blastxml.pm in @INC (you may need to install the Bio::SearchIO::blastxml module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Bio/Root/Root.pm line 518.
For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Something went wrong running ../bin/parseXMLblast.pl: Can't call method "next_result" on an undefined value at ../bin/parseXMLblast.pl line 76. -- fatal.
As mentioned in the error, I installed Bio::SearchIO::blastxml using cpanm, but it still throws me the same error. Could you please point out what am I doing wrong?
Thanks and regards Anchal
blastall is wublast, which isn't compatible with the parseXMLblast.pl parser.
Please download and install NCBI blast on your system.
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
note: hlaminer has NOT been tested with versions newer than 2-2-29
Hello Warren,
I installed blast as follows:
sudo apt update sudo apt install ncbi-blast+ -y
and it got installed all fine. I can also access blastn. I also modified the path for blastn in ncbiBlastConfig2-2-29.txt file to /usr/bin/blastn. But when I am running the parseXMLblast.pl it is still giving me the same error.
"Bio::SearchIO: blastxml cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate Bio/SearchIO/blastxml.pm in @INC (you may need to install the Bio::SearchIO::blastxml module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Bio/Root/Root.pm line 518.
For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Something went wrong running ../bin/parseXMLblast.pl: Can't call method "next_result" on an undefined value at ../bin/parseXMLblast.pl line 76. -- fatal. USAGE blastn [-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] [-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] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version]
DESCRIPTION Nucleotide-Nucleotide BLAST 2.6.0+
Error: Unknown argument: "d" Error: (CArgException::eInvalidArg) Unknown argument: "d" "
I am unable to figure this out.
you'll need to install bioperl. parseXMLblast.pl requires this library
"Bio::SearchIO"
I already did that as follows:
git clone https://github.com/pcantalupo/Bundle-Bio-SearchIO.git
cd Bundle-Bio-SearchIO/
apt-cache search module-Build-perl
sudo apt-get install libmodule-build-perl
sudo apt update
sudo apt install bioperl -y
perl Build.PL
and then I installed blastxml also as follows:
cpanm Bio::SearchIO::blastxml
--> Working on Bio::SearchIO::blastxml
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/Bio-SearchIO-blastxml-1.70.tar.gz ... OK
Configuring Bio-SearchIO-blastxml-1.70 ... OK
Building and testing Bio-SearchIO-blastxml-1.70 ... OK
Successfully installed Bio-SearchIO-blastxml-1.70
1 distribution installed
Although it shows 1 distribution installed but I am unable to access blastxml.
looks like it's unaware of its path. You could edit the parseXML script as follows:
use lib /path-to-bioperl/
My apologies for bugging so much, but I do not code in perl at all. I tried to edit the script as you suggested but I think I did not do it properly. The path where my perl is installed is /mnt/softwares/Bundle-Bio-SearchIO/. I added this path before Bio::SearchIO as follows:
`use lib "/mnt/softwares/Bundle-Bio-SearchIO/Bio::SearchIO";
`
But now it is throwing error about line 74 which is :
my $in = Bio::SearchIO->new(-format => 'blastxml', -fh => $fh);
I tried adding the path here as well but I am not doing it right. Could you please guide me as to how to specify path here?
you need:
use lib "/mnt/softwares/Bundle-Bio-SearchIO/";
use Bio::SearchIO;
I managed to solve the issue with Bio::SearchIO, but now it is throwing me following error:
perl ../bin/parseXMLblast.pl -c ncbiBlastConfig2-2-29.txt -d ../database/HLA_ABC_CDS.fasta -i TASRhla200.contigs -o 0 -a 1 > tig_vs_hla-ncbi.coord
USAGE blastn [-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] [-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] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version]
DESCRIPTION Nucleotide-Nucleotide BLAST 2.6.0+
Error: Unknown argument: "d" Error: (CArgException::eInvalidArg) Unknown argument: "d"
How to go about it?
the error message tells me you've installed ncbi BLAST 2.6.0+, which has never been tested with HLAminer.
As I mentioned 2 days ago:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
note: hlaminer has NOT been tested with versions newer than 2-2-29
So, please download+install ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ in order to use hlaminer.
I regret that this project is no longer actively developed. As a consequence, newer versions of software/dependencies are NOT supported.
Hello,
I am installing HLAminer and as part of it I was trying to run HLAminer on test dataset. Everything works fine apart from aligning TASR contigs to HLA reference with following command:
perl ../bin/parseXMLblast.pl -cncbiBlastConfigO.txt -d ../database/HLA_ABC_CDS.fasta -i TASRhla200.contigs -o 0 -a 1 > tig_vs_hla-ncbi.coord
When I run this, it ends in following error:
File ncbiBlastConfigO.txt doesn't exist
There is no such file in either bin or test_demo directory. I tried changing the names to ncbiBlastConfig2-2-29.txt and ncbiBlastConfig2-2-28.txt files also, but still it doesn't work. It gives following error:
Can't find executable /Users/rwarren/biosw/ncbi-blast-2.2.29+/bin/blastn as indicated in ncbiBlastConfig2-2-29.txt --fatal.
Could you please suggest how to go about it?
Regards Anchal