From sammy.ich17 at gmail.com Mon Nov 10 12:27:34 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Mon, 10 Nov 2014 12:27:34 +0100 Subject: [Inparanoid] offline blast parameters when setting run_blast = 0 Message-ID: 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)? Next, when setting $run_blast = 0 the blastall results should already be parsed? Thanks. Sammy -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Nov 10 13:49:04 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 10 Nov 2014 13:49:04 +0100 Subject: [Inparanoid] offline blast parameters when setting run_blast = 0 In-Reply-To: References: Message-ID: <5460B440.4070807@scilifelab.se> 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 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: From erik.sonnhammer at scilifelab.se Mon Nov 10 17:43:40 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 10 Nov 2014 17:43:40 +0100 Subject: [Inparanoid] offline blast parameters when setting run_blast = 0 In-Reply-To: References: <5460B440.4070807@scilifelab.se> Message-ID: <5460EB3C.6050307@scilifelab.se> 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 > > > 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 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: From sammy.ich17 at gmail.com Fri Nov 14 11:58:07 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Fri, 14 Nov 2014 11:58:07 +0100 Subject: [Inparanoid] offline blast parameters when setting run_blast = 0 In-Reply-To: <5460EB3C.6050307@scilifelab.se> References: <5460B440.4070807@scilifelab.se> <5460EB3C.6050307@scilifelab.se> Message-ID: 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 >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sgadag at midwestern.edu Tue Nov 18 01:46:28 2014 From: sgadag at midwestern.edu (Gadagkar, Sudhindra) Date: Tue, 18 Nov 2014 00:46:28 +0000 Subject: [Inparanoid] Software error on Inparanoid Message-ID: <7B24B9F1CAA4684AB3EE492588514B543EFB5732@AZGLMBX01.midwestern.edu> Hello, I received the following error when I tried to do a search by Sequence ID for the Mouse GeneID, MGI:2148705 (for FOXP2, which I obtained from Inparanoid). Software error: at /var/www/inparanoid51.sbc.su.se/inparanoidweb/cgi-bin/gene_search.cgi line 26. For help, please send mail to the webmaster (root at localhost), giving this error message and the time and date of the error. Any help would be appreciated. I need the orthologs (Ensembl IDs for the orthologs would be sufficient) I reproduce here a screenshot of my text search: [cid:image002.png at 01D0028E.4F8F0910] Thanks, Sudhindra R. Gadagkar, Ph.D. _________________________________________________________________ Biomedical Sciences Midwestern University 19555 North 59th Avenue Glendale, AZ 85308 Tel: (623) 572-3855 Fax: (623) 572-3647 Email: sgadagkar at midwestern.edu _________________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 238447 bytes Desc: image002.png URL: From rtrichainfo at gmail.com Fri Nov 21 05:54:49 2014 From: rtrichainfo at gmail.com (Richa T) Date: Thu, 21 Nov 2014 04:54:49 +0000 Subject: [Inparanoid] =?iso-8859-1?q?FW=3A=09inparanoid?= Message-ID: http://www.privateyachtcharter-sxm.com/escpcj/lxhvvhgksrwiqjpvqlggvwfngfljgfiukaxfxo.nlyepcpfcqykckwncnysuihodewdssuzxtwuric Richa T -------------- next part -------------- An HTML attachment was scrubbed... URL: