From francesco.cicconardi at uibk.ac.at Tue Jun 3 10:15:13 2014 From: francesco.cicconardi at uibk.ac.at (Francesco Cicconardi) Date: Tue, 3 Jun 2014 10:15:13 +0200 Subject: [Inparanoid] BLAST 2.2.25+ Message-ID: Dears, I just downloaded the stand alone version of InParanoid v4.1. Reading the read me it looks like the program uses blastall and formatdb, since the newer version of Blast, the v2.2.25+ is not using anymore the two, how could I modify the perl script? Which lines and how? Thank you very much Francesco _________________________________________________ Francesco Cicconardi, Ph.D. University of Innsbruck Institute of Ecology Research Group: Molecular Ecology , Personal web page Technikerstrasse 25 A-6020 Innsbruck Tel: +43 (0)512 507-51767 Fax: +43 (0)512 507-51799 E-mail: francesco.cicconardi at uibk.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From mateusz.kaduk at gmail.com Wed Jun 4 13:34:13 2014 From: mateusz.kaduk at gmail.com (mateusz.kaduk at gmail.com) Date: Wed, 4 Jun 2014 13:34:13 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: Message-ID: Dear Francesco, There are two versions of blast, one named blast2 2.2.26 which is older version, and newest ncbi-blast+ 2.2.28 The differences are (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb However they produce exactly the same files, and files are exchangeable For example makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa formatdb -i c.albicans.fa are equivalent (2) Also blast results are the same for both blast2 2.2.26 and 2.2.28 (at least for dataset 5428 sequences from c.albicans and 4722 from s.cerevisiae, and other smaller dataset). blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M BLOSUM62 -z 5000000 -m8 > blast2.txt blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 6 > blast+.txt diff blast2.txt blast+.txt # Blast results in tab-delimited format are the same for both (3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz ~12m37 blast2 2.2.26 ~13m15 ncbi-blast+ 2.2.28 Therefore I don't think there is any advantage of using newer version of blast for the purpose of InParanoid. We might update that in future, but for now if you really want to use ncbi-blast+ feel free to modify the script, three commands below, provide compatible blast results, however you need to replace FILE,TARGET,QUERY,OUTPUT with the right variable names in the inparanoid.pl script (that might work). makeblastdb -in FILE -dbtype prot -out FILE blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 -seg no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT However, I suggest sticking with blast2 2.2.26 which is what current version of inparanoid depends on and is tested with. If you're using Debian based GNU/Linux distribution at this moment newest blast2 is 2.2.26 and you can install it from repository by "apt-get install blast2" Kind regards, Mateusz On 3 June 2014 10:15, Francesco Cicconardi wrote: > Dears, > > I just downloaded the stand alone version of InParanoid v4.1. Reading the > read me it looks like the program uses blastall and formatdb, since the > newer version of Blast, the v2.2.25+ is not using anymore the two, how > could I modify the perl script? Which lines and how? > > Thank you very much > Francesco > > > > > _________________________________________________ > > Francesco Cicconardi, Ph.D. > > University of Innsbruck > Institute of Ecology > > Research Group: Molecular Ecology > , Personal > web page > > Technikerstrasse 25 > A-6020 Innsbruck > > Tel: +43 (0)512 507-51767 > Fax: +43 (0)512 507-51799 > E-mail: francesco.cicconardi at uibk.ac.at > > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mateusz.kaduk at gmail.com Fri Jun 6 11:40:03 2014 From: mateusz.kaduk at gmail.com (mateusz.kaduk at gmail.com) Date: Fri, 6 Jun 2014 11:40:03 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Dear Francesco, It could be your script/modification not working properly. I tried running original inparanoid with your dataset, and it works as expected (See file in attachment). Is there any good reason, why you cannot use supported blast2 versions (like 2.2.25, 2.2.26)? Mateusz On 6 June 2014 10:59, Francesco Cicconardi wrote: > Dear Mateusz, > > I think there is something wrong with the blast_parser.pl. When I execute > this command: > > legacy_blast.pl blastall --path /usr/local/ncbi/blast/bin -F\"m S\" -i > dnig -z 5000000 -d dnig -p blastp -M BLOSUM62 -m7 | ./blast_parser.pl 0 -a > > It gives me this error: > > not well-formed (invalid token) at line 1, column 3017, byte 3017 at ./ > blast_parser.pl line 105. > > Program failed, try executing the command manually. > > > The blast command works since with another dataset it works perfectly > > Attached you may find a test dataset not working. > > > Cheers > > Francesco > > > > > 2014-06-06 10:18 GMT+02:00 Francesco Cicconardi : > > Dear Mateusz, >> >> Sorry to disturb you again. I have a strange problem with inparanoid on >> my data. It gives me the following error "Blast output file A->A is >> missing" and that dataset is my. I could it be that a blast search on >> itself gives an empty file? >> >> Thank you very much >> Francesco >> >> >> >> 2014-06-04 13:45 GMT+02:00 Francesco Cicconardi : >> >> Dear Mateusz, >>> >>> Thank you for your detailed answer, I was able to modify the script >>> changing "makeblastdb" and adding "legacy_blast.pl" to the blastall >>> command... it works!!! >>> >>> Thank you again >>> Francesco >>> >>> >>> 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com < >>> mateusz.kaduk at gmail.com>: >>> >>> Dear Francesco, >>>> >>>> There are two versions of blast, one named blast2 2.2.26 which is >>>> older version, and newest ncbi-blast+ 2.2.28 >>>> >>>> The differences are >>>> >>>> (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb >>>> >>>> However they produce exactly the same files, and files are >>>> exchangeable >>>> >>>> For example >>>> makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa >>>> formatdb -i c.albicans.fa >>>> >>>> are equivalent >>>> >>>> (2) Also blast results are the same for both blast2 2.2.26 and 2.2.28 >>>> (at least for dataset 5428 sequences from c.albicans and 4722 from >>>> s.cerevisiae, and other smaller dataset). >>>> >>>> blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M >>>> BLOSUM62 -z 5000000 -m8 > blast2.txt >>>> blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 >>>> -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize >>>> 5000000 -outfmt 6 > blast+.txt >>>> >>>> diff blast2.txt blast+.txt # Blast results in tab-delimited >>>> format are the same for both >>>> >>>> (3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz >>>> >>>> ~12m37 blast2 2.2.26 >>>> ~13m15 ncbi-blast+ 2.2.28 >>>> >>>> Therefore I don't think there is any advantage of using newer version >>>> of blast for the purpose of InParanoid. We might update that in future, but >>>> for now if you really want to use ncbi-blast+ feel free to modify the >>>> script, three commands below, provide compatible blast results, however you >>>> need to replace FILE,TARGET,QUERY,OUTPUT with the right variable names in >>>> the inparanoid.pl script (that might work). >>>> >>>> makeblastdb -in FILE -dbtype prot -out FILE >>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 >>>> -seg yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>> OUTPUT >>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 >>>> -seg no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>> OUTPUT >>>> >>>> However, I suggest sticking with blast2 2.2.26 which is what current >>>> version of inparanoid depends on and is tested with. >>>> >>>> If you're using Debian based GNU/Linux distribution at this moment >>>> newest blast2 is 2.2.26 and you can install it from repository by "apt-get >>>> install blast2" >>>> >>>> Kind regards, >>>> Mateusz >>>> >>>> >>>> On 3 June 2014 10:15, Francesco Cicconardi < >>>> francesco.cicconardi at uibk.ac.at> wrote: >>>> >>>>> Dears, >>>>> >>>>> I just downloaded the stand alone version of InParanoid v4.1. >>>>> Reading the read me it looks like the program uses blastall and formatdb, >>>>> since the newer version of Blast, the v2.2.25+ is not using anymore the >>>>> two, how could I modify the perl script? Which lines and how? >>>>> >>>>> Thank you very much >>>>> Francesco >>>>> >>>>> >>>>> >>>>> >>>>> _________________________________________________ >>>>> >>>>> Francesco Cicconardi, Ph.D. >>>>> >>>>> University of Innsbruck >>>>> Institute of Ecology >>>>> >>>>> Research Group: Molecular Ecology >>>>> , Personal >>>>> web page >>>>> >>>>> >>>>> Technikerstrasse 25 >>>>> A-6020 Innsbruck >>>>> >>>>> Tel: +43 (0)512 507-51767 >>>>> Fax: +43 (0)512 507-51799 >>>>> E-mail: francesco.cicconardi at uibk.ac.at >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> InParanoid mailing list >>>>> InParanoid at lists.su.se >>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- mateusz at astro:~/Francesco$ ls dnig inparanoid_4.1.tgz mateusz at astro:~/Francesco$ tar xvfz inparanoid_4.1.tgz inparanoid_4.1/ inparanoid_4.1/EC inparanoid_4.1/README inparanoid_4.1/seqstat.jar inparanoid_4.1/PAM30 inparanoid_4.1/PAM70 inparanoid_4.1/LICENCE inparanoid_4.1/BLOSUM45 inparanoid_4.1/blast_parser.pl inparanoid_4.1/LicenseAgreement.txt inparanoid_4.1/SC inparanoid_4.1/BLOSUM80 inparanoid_4.1/inparanoid.pl inparanoid_4.1/BLOSUM62 mateusz at astro:~/Francesco$ cd inparanoid_4.1/ mateusz at astro:~/Francesco/inparanoid_4.1$ mv ../dnig ./ mateusz at astro:~/Francesco/inparanoid_4.1$ ./inparanoid.pl dnig EC 250 sequences in file dnig 200 sequences in file EC 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 dnig - dnig on Fri Jun 6 11:13:08 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for dnig - dnig on Fri Jun 6 11:13:10 CEST 2014 Starting first BLAST pass for dnig - EC on Fri Jun 6 11:13:19 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for dnig - EC on Fri Jun 6 11:13:19 CEST 2014 Starting first BLAST pass for EC - dnig on Fri Jun 6 11:13:20 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for EC - dnig on Fri Jun 6 11:13:20 CEST 2014 Starting first BLAST pass for EC - EC on Fri Jun 6 11:13:21 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for EC - EC on Fri Jun 6 11:13:35 CEST 2014 Done BLAST searches. Starting ortholog detection... Output saved to file Output.dnig-EC HTML output saved to orthologs.dnig-EC.html Table output saved to table.dnig-EC mysql output saved to sqltable.dnig-EC mateusz at astro:~/Francesco/inparanoid_4.1$ wc sqltable.dnig-EC 2 12 71 sqltable.dnig-EC mateusz at astro:~/Francesco/inparanoid_4.1$ cat sqltable.dnig-EC 1 465 dnig 1.000 comp36696_c0_seq1 100% 1 465 EC 1.000 ADH3_ECOLI 100% mateusz at astro:~/Francesco/inparanoid_4.1$ From francicco at gmail.com Wed Jun 4 13:45:14 2014 From: francicco at gmail.com (Francesco Cicconardi) Date: Wed, 4 Jun 2014 13:45:14 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Dear Mateusz, Thank you for your detailed answer, I was able to modify the script changing "makeblastdb" and adding "legacy_blast.pl" to the blastall command... it works!!! Thank you again Francesco 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com : > Dear Francesco, > > There are two versions of blast, one named blast2 2.2.26 which is older > version, and newest ncbi-blast+ 2.2.28 > > The differences are > > (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb > > However they produce exactly the same files, and files are exchangeable > > For example > makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa > formatdb -i c.albicans.fa > > are equivalent > > (2) Also blast results are the same for both blast2 2.2.26 and 2.2.28 > (at least for dataset 5428 sequences from c.albicans and 4722 from > s.cerevisiae, and other smaller dataset). > > blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M > BLOSUM62 -z 5000000 -m8 > blast2.txt > blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 > -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize > 5000000 -outfmt 6 > blast+.txt > > diff blast2.txt blast+.txt # Blast results in tab-delimited format > are the same for both > > (3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz > > ~12m37 blast2 2.2.26 > ~13m15 ncbi-blast+ 2.2.28 > > Therefore I don't think there is any advantage of using newer version of > blast for the purpose of InParanoid. We might update that in future, but > for now if you really want to use ncbi-blast+ feel free to modify the > script, three commands below, provide compatible blast results, however you > need to replace FILE,TARGET,QUERY,OUTPUT with the right variable names in > the inparanoid.pl script (that might work). > > makeblastdb -in FILE -dbtype prot -out FILE > blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 -seg > yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT > blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 -seg > no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT > > However, I suggest sticking with blast2 2.2.26 which is what current > version of inparanoid depends on and is tested with. > > If you're using Debian based GNU/Linux distribution at this moment newest > blast2 is 2.2.26 and you can install it from repository by "apt-get install > blast2" > > Kind regards, > Mateusz > > > On 3 June 2014 10:15, Francesco Cicconardi < > francesco.cicconardi at uibk.ac.at> wrote: > >> Dears, >> >> I just downloaded the stand alone version of InParanoid v4.1. Reading >> the read me it looks like the program uses blastall and formatdb, since the >> newer version of Blast, the v2.2.25+ is not using anymore the two, how >> could I modify the perl script? Which lines and how? >> >> Thank you very much >> Francesco >> >> >> >> >> _________________________________________________ >> >> Francesco Cicconardi, Ph.D. >> >> University of Innsbruck >> Institute of Ecology >> >> Research Group: Molecular Ecology >> , Personal >> web page >> >> Technikerstrasse 25 >> A-6020 Innsbruck >> >> Tel: +43 (0)512 507-51767 >> Fax: +43 (0)512 507-51799 >> E-mail: francesco.cicconardi at uibk.ac.at >> >> >> _______________________________________________ >> InParanoid mailing list >> InParanoid at lists.su.se >> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francicco at gmail.com Fri Jun 6 10:18:07 2014 From: francicco at gmail.com (Francesco Cicconardi) Date: Fri, 6 Jun 2014 10:18:07 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Dear Mateusz, Sorry to disturb you again. I have a strange problem with inparanoid on my data. It gives me the following error "Blast output file A->A is missing" and that dataset is my. I could it be that a blast search on itself gives an empty file? Thank you very much Francesco 2014-06-04 13:45 GMT+02:00 Francesco Cicconardi : > Dear Mateusz, > > Thank you for your detailed answer, I was able to modify the script > changing "makeblastdb" and adding "legacy_blast.pl" to the blastall > command... it works!!! > > Thank you again > Francesco > > > 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com < > mateusz.kaduk at gmail.com>: > > Dear Francesco, >> >> There are two versions of blast, one named blast2 2.2.26 which is older >> version, and newest ncbi-blast+ 2.2.28 >> >> The differences are >> >> (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb >> >> However they produce exactly the same files, and files are exchangeable >> >> For example >> makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa >> formatdb -i c.albicans.fa >> >> are equivalent >> >> (2) Also blast results are the same for both blast2 2.2.26 and 2.2.28 >> (at least for dataset 5428 sequences from c.albicans and 4722 from >> s.cerevisiae, and other smaller dataset). >> >> blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M >> BLOSUM62 -z 5000000 -m8 > blast2.txt >> blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 >> -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize >> 5000000 -outfmt 6 > blast+.txt >> >> diff blast2.txt blast+.txt # Blast results in tab-delimited format >> are the same for both >> >> (3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz >> >> ~12m37 blast2 2.2.26 >> ~13m15 ncbi-blast+ 2.2.28 >> >> Therefore I don't think there is any advantage of using newer version >> of blast for the purpose of InParanoid. We might update that in future, but >> for now if you really want to use ncbi-blast+ feel free to modify the >> script, three commands below, provide compatible blast results, however you >> need to replace FILE,TARGET,QUERY,OUTPUT with the right variable names in >> the inparanoid.pl script (that might work). >> >> makeblastdb -in FILE -dbtype prot -out FILE >> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 -seg >> yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT >> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 -seg >> no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT >> >> However, I suggest sticking with blast2 2.2.26 which is what current >> version of inparanoid depends on and is tested with. >> >> If you're using Debian based GNU/Linux distribution at this moment newest >> blast2 is 2.2.26 and you can install it from repository by "apt-get install >> blast2" >> >> Kind regards, >> Mateusz >> >> >> On 3 June 2014 10:15, Francesco Cicconardi < >> francesco.cicconardi at uibk.ac.at> wrote: >> >>> Dears, >>> >>> I just downloaded the stand alone version of InParanoid v4.1. Reading >>> the read me it looks like the program uses blastall and formatdb, since the >>> newer version of Blast, the v2.2.25+ is not using anymore the two, how >>> could I modify the perl script? Which lines and how? >>> >>> Thank you very much >>> Francesco >>> >>> >>> >>> >>> _________________________________________________ >>> >>> Francesco Cicconardi, Ph.D. >>> >>> University of Innsbruck >>> Institute of Ecology >>> >>> Research Group: Molecular Ecology >>> , Personal >>> web page >>> >>> >>> Technikerstrasse 25 >>> A-6020 Innsbruck >>> >>> Tel: +43 (0)512 507-51767 >>> Fax: +43 (0)512 507-51799 >>> E-mail: francesco.cicconardi at uibk.ac.at >>> >>> >>> >>> _______________________________________________ >>> InParanoid mailing list >>> InParanoid at lists.su.se >>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francicco at gmail.com Fri Jun 6 10:59:37 2014 From: francicco at gmail.com (Francesco Cicconardi) Date: Fri, 6 Jun 2014 10:59:37 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Dear Mateusz, I think there is something wrong with the blast_parser.pl. When I execute this command: legacy_blast.pl blastall --path /usr/local/ncbi/blast/bin -F\"m S\" -i dnig -z 5000000 -d dnig -p blastp -M BLOSUM62 -m7 | ./blast_parser.pl 0 -a It gives me this error: not well-formed (invalid token) at line 1, column 3017, byte 3017 at ./ blast_parser.pl line 105. Program failed, try executing the command manually. The blast command works since with another dataset it works perfectly Attached you may find a test dataset not working. Cheers Francesco 2014-06-06 10:18 GMT+02:00 Francesco Cicconardi : > Dear Mateusz, > > Sorry to disturb you again. I have a strange problem with inparanoid on my > data. It gives me the following error "Blast output file A->A is missing" > and that dataset is my. I could it be that a blast search on itself gives > an empty file? > > Thank you very much > Francesco > > > > 2014-06-04 13:45 GMT+02:00 Francesco Cicconardi : > > Dear Mateusz, >> >> Thank you for your detailed answer, I was able to modify the script >> changing "makeblastdb" and adding "legacy_blast.pl" to the blastall >> command... it works!!! >> >> Thank you again >> Francesco >> >> >> 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com < >> mateusz.kaduk at gmail.com>: >> >> Dear Francesco, >>> >>> There are two versions of blast, one named blast2 2.2.26 which is older >>> version, and newest ncbi-blast+ 2.2.28 >>> >>> The differences are >>> >>> (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb >>> >>> However they produce exactly the same files, and files are exchangeable >>> >>> For example >>> makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa >>> formatdb -i c.albicans.fa >>> >>> are equivalent >>> >>> (2) Also blast results are the same for both blast2 2.2.26 and 2.2.28 >>> (at least for dataset 5428 sequences from c.albicans and 4722 from >>> s.cerevisiae, and other smaller dataset). >>> >>> blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M >>> BLOSUM62 -z 5000000 -m8 > blast2.txt >>> blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 >>> -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize >>> 5000000 -outfmt 6 > blast+.txt >>> >>> diff blast2.txt blast+.txt # Blast results in tab-delimited >>> format are the same for both >>> >>> (3) Run time is also very similar on 3 out of 4 cores computer 2.66Ghz >>> >>> ~12m37 blast2 2.2.26 >>> ~13m15 ncbi-blast+ 2.2.28 >>> >>> Therefore I don't think there is any advantage of using newer version >>> of blast for the purpose of InParanoid. We might update that in future, but >>> for now if you really want to use ncbi-blast+ feel free to modify the >>> script, three commands below, provide compatible blast results, however you >>> need to replace FILE,TARGET,QUERY,OUTPUT with the right variable names in >>> the inparanoid.pl script (that might work). >>> >>> makeblastdb -in FILE -dbtype prot -out FILE >>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 -seg >>> yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT >>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 -seg >>> no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out OUTPUT >>> >>> However, I suggest sticking with blast2 2.2.26 which is what current >>> version of inparanoid depends on and is tested with. >>> >>> If you're using Debian based GNU/Linux distribution at this moment >>> newest blast2 is 2.2.26 and you can install it from repository by "apt-get >>> install blast2" >>> >>> Kind regards, >>> Mateusz >>> >>> >>> On 3 June 2014 10:15, Francesco Cicconardi < >>> francesco.cicconardi at uibk.ac.at> wrote: >>> >>>> Dears, >>>> >>>> I just downloaded the stand alone version of InParanoid v4.1. Reading >>>> the read me it looks like the program uses blastall and formatdb, since the >>>> newer version of Blast, the v2.2.25+ is not using anymore the two, how >>>> could I modify the perl script? Which lines and how? >>>> >>>> Thank you very much >>>> Francesco >>>> >>>> >>>> >>>> >>>> _________________________________________________ >>>> >>>> Francesco Cicconardi, Ph.D. >>>> >>>> University of Innsbruck >>>> Institute of Ecology >>>> >>>> Research Group: Molecular Ecology >>>> , Personal >>>> web page >>>> >>>> >>>> Technikerstrasse 25 >>>> A-6020 Innsbruck >>>> >>>> Tel: +43 (0)512 507-51767 >>>> Fax: +43 (0)512 507-51799 >>>> E-mail: francesco.cicconardi at uibk.ac.at >>>> >>>> >>>> >>>> _______________________________________________ >>>> InParanoid mailing list >>>> InParanoid at lists.su.se >>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dnig Type: application/octet-stream Size: 78293 bytes Desc: not available URL: From francicco at gmail.com Fri Jun 6 11:43:11 2014 From: francicco at gmail.com (Francesco Cicconardi) Date: Fri, 6 Jun 2014 11:43:11 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Having several programs that do the same things it a bit annoying to me... but I'll try. I don't understand why with the other datasets it works fine. Thank you anyway I'll let you know whether everything is then working All the best F 2014-06-06 11:40 GMT+02:00 mateusz.kaduk at gmail.com : > Dear Francesco, > > It could be your script/modification not working properly. I tried running > original inparanoid with your dataset, and it works as expected (See file > in attachment). > > Is there any good reason, why you cannot use supported blast2 versions > (like 2.2.25, 2.2.26)? > > Mateusz > > > > On 6 June 2014 10:59, Francesco Cicconardi wrote: > >> Dear Mateusz, >> >> I think there is something wrong with the blast_parser.pl. When I >> execute this command: >> >> legacy_blast.pl blastall --path /usr/local/ncbi/blast/bin -F\"m S\" -i >> dnig -z 5000000 -d dnig -p blastp -M BLOSUM62 -m7 | ./blast_parser.pl 0 >> -a >> >> It gives me this error: >> >> not well-formed (invalid token) at line 1, column 3017, byte 3017 at ./ >> blast_parser.pl line 105. >> >> Program failed, try executing the command manually. >> >> >> The blast command works since with another dataset it works perfectly >> >> Attached you may find a test dataset not working. >> >> >> Cheers >> >> Francesco >> >> >> >> >> 2014-06-06 10:18 GMT+02:00 Francesco Cicconardi : >> >> Dear Mateusz, >>> >>> Sorry to disturb you again. I have a strange problem with inparanoid on >>> my data. It gives me the following error "Blast output file A->A is >>> missing" and that dataset is my. I could it be that a blast search on >>> itself gives an empty file? >>> >>> Thank you very much >>> Francesco >>> >>> >>> >>> 2014-06-04 13:45 GMT+02:00 Francesco Cicconardi : >>> >>> Dear Mateusz, >>>> >>>> Thank you for your detailed answer, I was able to modify the script >>>> changing "makeblastdb" and adding "legacy_blast.pl" to the blastall >>>> command... it works!!! >>>> >>>> Thank you again >>>> Francesco >>>> >>>> >>>> 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com < >>>> mateusz.kaduk at gmail.com>: >>>> >>>> Dear Francesco, >>>>> >>>>> There are two versions of blast, one named blast2 2.2.26 which is >>>>> older version, and newest ncbi-blast+ 2.2.28 >>>>> >>>>> The differences are >>>>> >>>>> (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb >>>>> >>>>> However they produce exactly the same files, and files are >>>>> exchangeable >>>>> >>>>> For example >>>>> makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa >>>>> formatdb -i c.albicans.fa >>>>> >>>>> are equivalent >>>>> >>>>> (2) Also blast results are the same for both blast2 2.2.26 and >>>>> 2.2.28 (at least for dataset 5428 sequences from c.albicans and 4722 from >>>>> s.cerevisiae, and other smaller dataset). >>>>> >>>>> blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M >>>>> BLOSUM62 -z 5000000 -m8 > blast2.txt >>>>> blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 >>>>> -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize >>>>> 5000000 -outfmt 6 > blast+.txt >>>>> >>>>> diff blast2.txt blast+.txt # Blast results in tab-delimited >>>>> format are the same for both >>>>> >>>>> (3) Run time is also very similar on 3 out of 4 cores computer >>>>> 2.66Ghz >>>>> >>>>> ~12m37 blast2 2.2.26 >>>>> ~13m15 ncbi-blast+ 2.2.28 >>>>> >>>>> Therefore I don't think there is any advantage of using newer >>>>> version of blast for the purpose of InParanoid. We might update that in >>>>> future, but for now if you really want to use ncbi-blast+ feel free to >>>>> modify the script, three commands below, provide compatible blast results, >>>>> however you need to replace FILE,TARGET,QUERY,OUTPUT with the right >>>>> variable names in the inparanoid.pl script (that might work). >>>>> >>>>> makeblastdb -in FILE -dbtype prot -out FILE >>>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 >>>>> -seg yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>>> OUTPUT >>>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 >>>>> -seg no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>>> OUTPUT >>>>> >>>>> However, I suggest sticking with blast2 2.2.26 which is what current >>>>> version of inparanoid depends on and is tested with. >>>>> >>>>> If you're using Debian based GNU/Linux distribution at this moment >>>>> newest blast2 is 2.2.26 and you can install it from repository by "apt-get >>>>> install blast2" >>>>> >>>>> Kind regards, >>>>> Mateusz >>>>> >>>>> >>>>> On 3 June 2014 10:15, Francesco Cicconardi < >>>>> francesco.cicconardi at uibk.ac.at> wrote: >>>>> >>>>>> Dears, >>>>>> >>>>>> I just downloaded the stand alone version of InParanoid v4.1. >>>>>> Reading the read me it looks like the program uses blastall and formatdb, >>>>>> since the newer version of Blast, the v2.2.25+ is not using anymore the >>>>>> two, how could I modify the perl script? Which lines and how? >>>>>> >>>>>> Thank you very much >>>>>> Francesco >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _________________________________________________ >>>>>> >>>>>> Francesco Cicconardi, Ph.D. >>>>>> >>>>>> University of Innsbruck >>>>>> Institute of Ecology >>>>>> >>>>>> Research Group: Molecular Ecology >>>>>> , Personal >>>>>> web page >>>>>> >>>>>> >>>>>> Technikerstrasse 25 >>>>>> A-6020 Innsbruck >>>>>> >>>>>> Tel: +43 (0)512 507-51767 >>>>>> Fax: +43 (0)512 507-51799 >>>>>> E-mail: francesco.cicconardi at uibk.ac.at >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> InParanoid mailing list >>>>>> InParanoid at lists.su.se >>>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francicco at gmail.com Fri Jun 6 12:05:11 2014 From: francicco at gmail.com (Francesco Cicconardi) Date: Fri, 6 Jun 2014 12:05:11 +0200 Subject: [Inparanoid] BLAST 2.2.25+ In-Reply-To: References: <13fea6678f44431fb57549c6bde368f8@XCAS1.uibk.ac.at> Message-ID: Ok Mateusz, Now everything's working perfectly. Thank you so much and sorry :) All the best F 2014-06-06 11:43 GMT+02:00 Francesco Cicconardi : > Having several programs that do the same things it a bit annoying to me... > but I'll try. > > I don't understand why with the other datasets it works fine. > > Thank you anyway > I'll let you know whether everything is then working > > All the best > F > > > 2014-06-06 11:40 GMT+02:00 mateusz.kaduk at gmail.com < > mateusz.kaduk at gmail.com>: > > Dear Francesco, >> >> It could be your script/modification not working properly. I tried >> running original inparanoid with your dataset, and it works as expected >> (See file in attachment). >> >> Is there any good reason, why you cannot use supported blast2 versions >> (like 2.2.25, 2.2.26)? >> >> Mateusz >> >> >> >> On 6 June 2014 10:59, Francesco Cicconardi wrote: >> >>> Dear Mateusz, >>> >>> I think there is something wrong with the blast_parser.pl. When I >>> execute this command: >>> >>> legacy_blast.pl blastall --path /usr/local/ncbi/blast/bin -F\"m S\" -i >>> dnig -z 5000000 -d dnig -p blastp -M BLOSUM62 -m7 | ./blast_parser.pl 0 >>> -a >>> >>> It gives me this error: >>> >>> not well-formed (invalid token) at line 1, column 3017, byte 3017 at ./ >>> blast_parser.pl line 105. >>> >>> Program failed, try executing the command manually. >>> >>> >>> The blast command works since with another dataset it works perfectly >>> >>> Attached you may find a test dataset not working. >>> >>> >>> Cheers >>> >>> Francesco >>> >>> >>> >>> >>> 2014-06-06 10:18 GMT+02:00 Francesco Cicconardi : >>> >>> Dear Mateusz, >>>> >>>> Sorry to disturb you again. I have a strange problem with inparanoid on >>>> my data. It gives me the following error "Blast output file A->A is >>>> missing" and that dataset is my. I could it be that a blast search on >>>> itself gives an empty file? >>>> >>>> Thank you very much >>>> Francesco >>>> >>>> >>>> >>>> 2014-06-04 13:45 GMT+02:00 Francesco Cicconardi : >>>> >>>> Dear Mateusz, >>>>> >>>>> Thank you for your detailed answer, I was able to modify the script >>>>> changing "makeblastdb" and adding "legacy_blast.pl" to the blastall >>>>> command... it works!!! >>>>> >>>>> Thank you again >>>>> Francesco >>>>> >>>>> >>>>> 2014-06-04 13:34 GMT+02:00 mateusz.kaduk at gmail.com < >>>>> mateusz.kaduk at gmail.com>: >>>>> >>>>> Dear Francesco, >>>>>> >>>>>> There are two versions of blast, one named blast2 2.2.26 which is >>>>>> older version, and newest ncbi-blast+ 2.2.28 >>>>>> >>>>>> The differences are >>>>>> >>>>>> (1) That blast2 uses formatdb and ncbi-blast+ uses makeblastdb >>>>>> >>>>>> However they produce exactly the same files, and files are >>>>>> exchangeable >>>>>> >>>>>> For example >>>>>> makeblastdb -in c.albicans.fa -dbtype prot -out c.albicans.fa >>>>>> formatdb -i c.albicans.fa >>>>>> >>>>>> are equivalent >>>>>> >>>>>> (2) Also blast results are the same for both blast2 2.2.26 and >>>>>> 2.2.28 (at least for dataset 5428 sequences from c.albicans and 4722 from >>>>>> s.cerevisiae, and other smaller dataset). >>>>>> >>>>>> blastall -C3 -F"m S" -i s.cerevisiae.fa -d c.albicans.fa -p blastp -M >>>>>> BLOSUM62 -z 5000000 -m8 > blast2.txt >>>>>> blastp -db c.albicans.fa -query s.cerevisiae.fa -matrix BLOSUM62 >>>>>> -comp_based_stats 3 -seg yes -soft_masking true -num_threads 3 -dbsize >>>>>> 5000000 -outfmt 6 > blast+.txt >>>>>> >>>>>> diff blast2.txt blast+.txt # Blast results in tab-delimited >>>>>> format are the same for both >>>>>> >>>>>> (3) Run time is also very similar on 3 out of 4 cores computer >>>>>> 2.66Ghz >>>>>> >>>>>> ~12m37 blast2 2.2.26 >>>>>> ~13m15 ncbi-blast+ 2.2.28 >>>>>> >>>>>> Therefore I don't think there is any advantage of using newer >>>>>> version of blast for the purpose of InParanoid. We might update that in >>>>>> future, but for now if you really want to use ncbi-blast+ feel free to >>>>>> modify the script, three commands below, provide compatible blast results, >>>>>> however you need to replace FILE,TARGET,QUERY,OUTPUT with the right >>>>>> variable names in the inparanoid.pl script (that might work). >>>>>> >>>>>> makeblastdb -in FILE -dbtype prot -out FILE >>>>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 3 >>>>>> -seg yes -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>>>> OUTPUT >>>>>> blastp -db TARGET -query QUERY -matrix BLOSUM62 -comp_based_stats 0 >>>>>> -seg no -soft_masking true -num_threads 3 -dbsize 5000000 -outfmt 5 -out >>>>>> OUTPUT >>>>>> >>>>>> However, I suggest sticking with blast2 2.2.26 which is what current >>>>>> version of inparanoid depends on and is tested with. >>>>>> >>>>>> If you're using Debian based GNU/Linux distribution at this moment >>>>>> newest blast2 is 2.2.26 and you can install it from repository by "apt-get >>>>>> install blast2" >>>>>> >>>>>> Kind regards, >>>>>> Mateusz >>>>>> >>>>>> >>>>>> On 3 June 2014 10:15, Francesco Cicconardi < >>>>>> francesco.cicconardi at uibk.ac.at> wrote: >>>>>> >>>>>>> Dears, >>>>>>> >>>>>>> I just downloaded the stand alone version of InParanoid v4.1. >>>>>>> Reading the read me it looks like the program uses blastall and formatdb, >>>>>>> since the newer version of Blast, the v2.2.25+ is not using anymore the >>>>>>> two, how could I modify the perl script? Which lines and how? >>>>>>> >>>>>>> Thank you very much >>>>>>> Francesco >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _________________________________________________ >>>>>>> >>>>>>> Francesco Cicconardi, Ph.D. >>>>>>> >>>>>>> University of Innsbruck >>>>>>> Institute of Ecology >>>>>>> >>>>>>> Research Group: Molecular Ecology >>>>>>> >>>>>>> , Personal web page >>>>>>> >>>>>>> >>>>>>> Technikerstrasse 25 >>>>>>> A-6020 Innsbruck >>>>>>> >>>>>>> Tel: +43 (0)512 507-51767 >>>>>>> Fax: +43 (0)512 507-51799 >>>>>>> E-mail: francesco.cicconardi at uibk.ac.at >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> InParanoid mailing list >>>>>>> InParanoid at lists.su.se >>>>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bbely at ebi.ac.uk Mon Jun 23 13:10:19 2014 From: bbely at ebi.ac.uk (Benoit BELY) Date: Mon, 23 Jun 2014 12:10:19 +0100 Subject: [Inparanoid] Cross-reference mapping to UniProtKB Message-ID: <53A80B1B.3020906@ebi.ac.uk> Hi there, I'm in charge of corss-references (Xrefs) in UniProtKB, and I noticed your mapping that you used to provide to us is not available any more. Could you have a look at it please and provide an up-to-date mapping please ? here the file I'm looking for : http://inparanoid.sbc.su.se/download/current/InParanoidUniProtXref.txt Regards -- Benoit BELY ---------------------------------------- Software Engineer - UniProt release production team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom PHONE:+ (0) 1223 49 2648 FAX:+ (0) 1223 494 468 URL:http://www.ebi.ac.uk/ ---------------------------------------- The urgent is done, the impossible is underway, miracles allow time