[Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse
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[Gmod-ajax] Error converting BAM to JSON for browsing in Jbrowse
 
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Hi,
I have a BAM file and when i execute the following command to convert the BAM to Json : $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" I get the following error; No index file for /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line 1940 I have installed the prerequisite installed for browsing BAM files in Jbrowse .I also have the corresponding reference file in Json and am able to browse in Jbrowse. Do we have to create any index for browsing BAM files in Jbrowse before we convert it to Json .Please help me in resolving the following error. Thanks, Sanjay -- Success is how many times u smile each day every day. ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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In the future, JBrowse will probably use the autoindexing option as
suggested by that error message. Right now, though, you can get around this by creating the index manually with samtools; you'd write something like: $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam (using the full path to the samtools program if it's not in your path) Mitch On 06/22/2010 02:12 AM, sanjay shah wrote: > Hi, > > I have a BAM file and when i execute the following command to > convert the BAM to Json : > > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > I get the following error; > > No index file for > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening > file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line > 1940 > > I have installed the prerequisite installed for browsing BAM files in > Jbrowse .I also have the corresponding reference file in Json and am > able to browse in Jbrowse. > > > Do we have to create any index for browsing BAM files in Jbrowse > before we convert it to Json .Please help me in resolving the > following error. > > > > Thanks, > Sanjay > > ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Hi ,
Thanks.I did sort the alignments and then created index manually with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I again try to convert BAM to JSON by issuing command as: $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" I get following error: Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. Please help on this aspect ..Thanks Thanks, Sanjay On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner <[hidden email]> wrote: > In the future, JBrowse will probably use the autoindexing option as > suggested by that error message. > > Right now, though, you can get around this by creating the index manually > with samtools; you'd write something like: > > $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam > > (using the full path to the samtools program if it's not in your path) > > Mitch > > On 06/22/2010 02:12 AM, sanjay shah wrote: >> >> Hi, >> >> I have a BAM file and when i execute the following command to >> convert the BAM to Json : >> >> $$ bin/flatfile-to-json.pl --bam >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >> --tracklabel BAM_data --key "BAM Data" >> >> I get the following error; >> >> No index file for >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >> 1940 >> >> I have installed the prerequisite installed for browsing BAM files in >> Jbrowse .I also have the corresponding reference file in Json and am >> able to browse in Jbrowse. >> >> >> Do we have to create any index for browsing BAM files in Jbrowse >> before we convert it to Json .Please help me in resolving the >> following error. >> >> >> >> Thanks, >> Sanjay >> >> > > -- Success is how many times u smile each day every day. ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Hi ,
Sorry Typo error in the earlier mail .. The bam file is "20100311.sorted.bam" and not "20100311.bam" that is being provided in the command after index has been created as : " 20100311.sorted.bam.bai .".. So the command executed is : $$ bin/flatfile-to-json.pl --bam /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon --tracklabel BAM_data --key "BAM Data" which throws the following error Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. Use of uninitialized value in subtraction (-) at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. Use of uninitialized value in int at /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. please help ..Thanks Thanks, Sanjay Thanks, Sanjay On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah <[hidden email]> wrote: > Hi , > > Thanks.I did sort the alignments and then created index manually > with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I > again try to convert BAM to JSON by issuing command as: > > > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > > I get following error: > > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. > > > > Please help on this aspect ..Thanks > > > Thanks, > Sanjay > > > On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner > <[hidden email]> wrote: >> In the future, JBrowse will probably use the autoindexing option as >> suggested by that error message. >> >> Right now, though, you can get around this by creating the index manually >> with samtools; you'd write something like: >> >> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam >> >> (using the full path to the samtools program if it's not in your path) >> >> Mitch >> >> On 06/22/2010 02:12 AM, sanjay shah wrote: >>> >>> Hi, >>> >>> I have a BAM file and when i execute the following command to >>> convert the BAM to Json : >>> >>> $$ bin/flatfile-to-json.pl --bam >>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >>> --tracklabel BAM_data --key "BAM Data" >>> >>> I get the following error; >>> >>> No index file for >>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >>> 1940 >>> >>> I have installed the prerequisite installed for browsing BAM files in >>> Jbrowse .I also have the corresponding reference file in Json and am >>> able to browse in Jbrowse. >>> >>> >>> Do we have to create any index for browsing BAM files in Jbrowse >>> before we convert it to Json .Please help me in resolving the >>> following error. >>> >>> >>> >>> Thanks, >>> Sanjay >>> >>> >> >> > > > > -- > Success is how many times u smile each day every day. > -- Success is how many times u smile each day every day. ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Hi,
I've seen this but I haven't yet figured out exactly what's going on. I think it has something to do with paired-end reads, and it might be caused by reads whose pair-mate isn't mapped. Handling paired-end reads better is something I'm currently working on. Mitch On 06/23/2010 01:35 AM, sanjay shah wrote: > Hi , > > > Sorry Typo error in the earlier mail .. > > The bam file is "20100311.sorted.bam" and not "20100311.bam" > that is being provided in the command after index has been created as > : > " 20100311.sorted.bam.bai .".. > So the command executed is : > $$ bin/flatfile-to-json.pl --bam > /var/www/jbrowse/docs/tutorial/data_files20100311.sorted.bam --cssclass exon > --tracklabel BAM_data --key "BAM Data" > > > which throws the following error > > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > Use of uninitialized value in subtraction (-) at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 25. > Use of uninitialized value in int at > /var/www/jbrowse_1/bin/../lib/JsonGenerator.pm line 27. > > > please help ..Thanks > > Thanks, > Sanjay > > > > > Thanks, > Sanjay > > On Wed, Jun 23, 2010 at 2:10 PM, sanjay shah<[hidden email]> wrote: > >> Hi , >> >> Thanks.I did sort the alignments and then created index manually >> with samtools( I have "20100311.sorted.bam.bai " file ) ; now when I >> again try to convert BAM to JSON by issuing command as: >> >> >> $$ bin/flatfile-to-json.pl --bam >> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >> --tracklabel BAM_data --key "BAM Data" >> >> >> I get following error: >> >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> Use of uninitialized value in int at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 27. >> Use of uninitialized value in subtraction (-) at >> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 25. >> >> >> >> Please help on this aspect ..Thanks >> >> >> Thanks, >> Sanjay >> >> >> On Tue, Jun 22, 2010 at 6:52 PM, Mitch Skinner >> <[hidden email]> wrote: >> >>> In the future, JBrowse will probably use the autoindexing option as >>> suggested by that error message. >>> >>> Right now, though, you can get around this by creating the index manually >>> with samtools; you'd write something like: >>> >>> $ samtools index /var/www/jbrowse/docs/tutorial/data_files/20100311.bam >>> >>> (using the full path to the samtools program if it's not in your path) >>> >>> Mitch >>> >>> On 06/22/2010 02:12 AM, sanjay shah wrote: >>> >>>> Hi, >>>> >>>> I have a BAM file and when i execute the following command to >>>> convert the BAM to Json : >>>> >>>> $$ bin/flatfile-to-json.pl --bam >>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam --cssclass exon >>>> --tracklabel BAM_data --key "BAM Data" >>>> >>>> I get the following error; >>>> >>>> No index file for >>>> /var/www/jbrowse/docs/tutorial/data_files/20100311.bam; try opening >>>> file with -autoindex at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line >>>> 1940 >>>> >>>> I have installed the prerequisite installed for browsing BAM files in >>>> Jbrowse .I also have the corresponding reference file in Json and am >>>> able to browse in Jbrowse. >>>> >>>> >>>> Do we have to create any index for browsing BAM files in Jbrowse >>>> before we convert it to Json .Please help me in resolving the >>>> following error. >>>> >>>> >>>> >>>> Thanks, >>>> Sanjay >>>> >>>> >>>> >>> >>> >> >> >> -- >> Success is how many times u smile each day every day. >> >> > > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Hi Mitch,
Thanks .But do that error really hampers the functionality of BAM files being visualized in Jbrowse(I mean is there any data ,information loss due to this in BAM to JSON conversion and visualization in Jbrowse. Thanks, Sanjay On Thu, Jul 1, 2010 at 8:12 PM, Mitch Skinner <[hidden email]> wrote: Hi, -- Success is how many times u smile each day every day. ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Mitch On 07/02/2010 12:01 AM, sanjay shah wrote: Hi Mitch, ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Re: Error converting BAM to JSON for browsing in Jbrowse
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Hi Mitch,
Thanks, Regards, Sanjay On Fri, Jul 2, 2010 at 6:47 PM, Mitch Skinner <[hidden email]> wrote:
-- Success is how many times u smile each day every day. ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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