[Inparanoid] BLAST 2.2.25+

Francesco Cicconardi francicco at gmail.com
Fri Jun 6 11:43:11 CEST 2014 

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 <francicco at gmail.com> 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 <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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140606/ad22124a/attachment-0001.html>

More information about the InParanoid mailing list