[Inparanoid] BLAST 2.2.25+

[Francesco Cicconardi]

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 <francicco at gmail.com>:

> 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 <francicco at gmail.com>:
>
> 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
>>>> <http://www.uibk.ac.at/ecology/forschung/molecular_ecology.html.en>, Personal
>>>> web page
>>>> <http://www.uibk.ac.at/ecology/staff/persons/cicconardi.html.en>
>>>>
>>>> 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
>>>> <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
>>>>
>>>>
>>>
>>
>
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