[Inparanoid] BLAST 2.2.25+

Francesco Cicconardi francicco at gmail.com
Fri Jun 6 12:05:11 CEST 2014 

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 <francicco at gmail.com>:

> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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