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Old 11-04-2011, 09:15 AM   #1
inou13
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Location: uk

Join Date: Sep 2010
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Default Breakdancer_max output is empty

HI ,

I am trying to use breakdancer for the first time and struggling a bit with the command lines
this is the version I have installed
breakdancer-1.1_2011_02_21

I have created my config file using
/breakdancer-1.1_2011_02_21/perl/bam2cfg.pl file#1.bam > file#1.bam.BD_config
this is the file
readgroup:NA platform:illumina map:file1#1.bam readlen:75.00 lib:NA num:9997 lower:32.49 upper:392.41 me
an:170.75 std:44.51 SWnormality:-54.43 exe:samtools view

hwne I run BreakdanceMax I create only the header of a file
/breakdancer-1.1_2011_02_21/cpp/breakdancer_max -t file#1.bam.BD_config >test.out

this is the test.out
#Command: /breakdancer-1.1_2011_02_21/cpp/breakdancer_max -t file#1.bam.BD_config
#Library Statistics:
#file#1.bam mean:170.75 std:44.51 uppercutoff:392.41 lowercutoff:32.49 readlen:75 library:NA reflen:303
9910766 seqcov:0.745619 phycov:0.848763 32:61859
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib file#1.bam

any clues/tips?
thanks a lot
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Old 12-21-2011, 10:31 PM   #2
liying
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Location: Beijing

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Default

Did you figure this out? And if you did, could you share the solution?
I also encountered this problem.
Thanks a lot!
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Old 12-26-2011, 04:11 AM   #3
jeny
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Join Date: Mar 2010
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Default

Do you have the index bam file corresponding to your bam in the same directory?
For troubleshooting, perl version of BreakDancerMax is helpful. Error message are more clear than C version.
Hope this help.
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Old 12-26-2011, 04:34 AM   #4
liying
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Location: Beijing

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hi,jeny
I do have the index file.
I may try perl version.
Thanks.

------------

I have tried the BreakDancerMax.pl. Unfortunately, the output was empty expect #header, too. And there was not any error information.

Thanks all the same.

Last edited by liying; 12-26-2011 at 10:31 PM.
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Old 04-25-2012, 04:54 PM   #5
caswater
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Join Date: Jun 2011
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have u guys figured it out? I just ran into the same problem
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