[Inparanoid] offline blast parameters when setting run_blast = 0

[Sammy Desilva]

Thanks for your help. I still have problems with parsing. First I run the
program in automated mode with $run_blast = 1 which gives me a file
file-AA_with_blast_on with 384412 lines. For the same data I used blast on
slurm then parsed the record for inparanoid input with $run_blast = 0. The
slurm blast/parsing resulted in file-AA_blast_off.fasta file which has only
4894 records.

I got the Parser Warning during the command
junk after document element at line 1, column 6899908, byte 6899908 at
blast_parser.pl line 105

This is the only command I used for parsing blastXML file
cat blastall_output | perl blast_parser.pl 40 >> file-AA_blast_off.fasta

for blastall I used the same parameters given in inparanoid.pl. Sir, please
let me know what I am doing wrong.

Thanks
Sammy

On Mon, Nov 10, 2014 at 5:43 PM, Erik Sonnhammer <
erik.sonnhammer at scilifelab.se> wrote:

>  Looks ok, but I don't know what that warning means.
>
> /Erik
>
>
> On 11/10/2014 05:36 PM, Sammy Desilva wrote:
>
> Thanks, please have a look whether the format of file-AA is correct  for
> input
>
> aml_g1t1    aml_g1t1    880.6    423    423    423    423    423    423
> q:1-423 h:1-423
> aml_g1t1    aml_g10385t1    150.6    423    301    210    248    210
> 248    q:1-210 h:39-286
> aml_g1t1    aml_g15430t1    98.6    423    162    139    137    139
> 137    q:1-139 h:3-139
> aml_g1t1    aml_g10384t1    89.0    423    620    132    128    132
> 128    q:266-397 h:15-142
> aml_g1t1    aml_g15143t1    85.5    423    246    108    107    108
> 107    q:301-408 h:16-122
> aml_g1t1    aml_g13567t1    81.3    423    376    112    104    112
> 104    q:306-417 h:181-284
> aml_g1t1    aml_g15245t1    67.0    423    153    95    94    95    94
> q:313-407 h:33-126
>
> Parser Warning
>
> junk after document element at line 1, column 6899908, byte 6899908 at
> blast_parser.pl line 105
>
> On Mon, Nov 10, 2014 at 1:49 PM, Erik Sonnhammer <
> erik.sonnhammer at scilifelab.se> wrote:
>
>>  On 11/10/2014 12:27 PM, Sammy Desilva wrote:
>>
>>  As mentioned in inparanoid.pl $run_blast could be set 0 if we have the
>> blast files. For the pairwise comparison of a big dataset I want to run the
>> blastall on cluster. Could you tell me which parameter-set of blastall I
>> should use so that there will be no difference in results (when $run_blast
>> is 1)?
>>
>>  Hi, simply use the same parameters ;)
>>
>> You can save compute time by running the "A-A" comparisons only once. If
>> you run the script for each species comparisons, A-A and B-B will be rerun
>> every time, so you almost save half the compute if you just do it once for
>> the whole batch.
>>
>>   Next, when setting $run_blast = 0 the blastall results should already
>> be parsed?
>>
>>  Yes.
>>
>> /Erik
>>
>>
>>  Thanks.
>>  Sammy
>>
>>
>> _______________________________________________
>> InParanoid mailing listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>
>>
>>
>
>
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