[Inparanoid] BLAST 2.2.25+

Fri Jun 6 11:40:03 CEST 2014

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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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$ 