Question: Problem to start Breakdancer
0
gravatar for dott.difranco
5 weeks ago by
dott.difranco0 wrote:

Hello everybody I'm new in this word of bionformatic and I'd want found structural variant on my bam file (that is stored in external HD) with breakdance. I've read this guide, but when I launch the first script:

/usr/lib/breakdancer-max1.2/bam2cfg.pl bam_files breakdancer_options

I've the file or directory not found. I've installed Perl v5.26.1

Where is my error? Thanks

sequence • 187 views
ADD COMMENTlink modified 5 weeks ago by RamRS27k • written 5 weeks ago by dott.difranco0
1

Either the bam2cfg.pl does not exist at the location above, or one or more of the BAM files do not exist. If there are any files that are part of the breakdancer_options parameter, check that they all exist too.

ADD REPLYlink written 5 weeks ago by RamRS27k

The file bam2cfg.pl exist in this path: home/marcoubu/breakdancer-master/perl/bam2cfg.pl. The file .bam exist too: media/sf_hd500gb/genoma S17-530.

ADD REPLYlink modified 5 weeks ago by RamRS27k • written 5 weeks ago by dott.difranco0
1

Can you please give us the exact command you're using?

ADD REPLYlink written 5 weeks ago by RamRS27k

I'm using this commad (from https://gmt.genome.wustl.edu/packages/breakdancer/documentation.html):

/usr/lib/breakdancer-max1.2/bam2cfg.pl bam_files breakdancer_options

Howerver, on going, I've seen that in /usr/lib I don't find the folder breakdancer-max1.2, but this is strange because the installation was successful. Also, I have seen that the file "bam2cfg.pl" is located only in /breakdancer/perl. What should I do to run the software? Thank you so much for your answers.

ADD REPLYlink written 5 weeks ago by dott.difranco0
2

That "command" is a template, it's not a real command. bam_files and breakdancer_options are placeholders for real parameter values. The command under STEP 1 is a real command (/usr/lib/breakdancer-max/bam2cfg.pl -g -h tumor.bam normal.bam > BRC6.cfg).

Your install location is different from the one specified in the manual. Your answer to where the .bam files exist doesn't seem accurate (unless you have a blank space in the directory name genoma S17-530. Your answer to where bam2cfg.pl exists seems to be inaccurate too (probably a copy-paste error - it might be /home/ and home/).

You'll need something along these lines:

/home/marcoubu/breakdancer-master/perl/bam2cfg.pl <path_to_actual_bam_file> <actual_breakdancer_options>
ADD REPLYlink written 5 weeks ago by RamRS27k

First of all thank you for the technical support. I haven't make past and cut.

So, I tried the following command (because my file bam is in this path /media/sf_hd500gb):

/home/marcoubu/breakdancer/perl/bam2cfg.pl /media/sf_hd500gb/genoma S17-530 actual_breakdancer_options

but I've this long error message:

/home/marcoubu/breakdancer/perl/bam2cfg.pl] Processing bam: /media/sf_hd500gb/genoma
[E::hts_open_format] Failed to open file /media/sf_hd500gb/genoma
samtools view: failed to open "/media/sf_hd500gb/genoma" for reading: No such file or directory
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing BAM file
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Send TERM signal for 27628
/home/marcoubu/breakdancer/perl/bam2cfg.pl] samtools pid process 27628 is still there...
/home/marcoubu/breakdancer/perl/bam2cfg.pl] invoking kill -9 on 27628 ...
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing samtools process : 27628
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Processing bam: S17-530
[E::hts_open_format] Failed to open file S17-530
samtools view: failed to open "S17-530" for reading: No such file or directory
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing BAM file
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Send TERM signal for 27629
/home/marcoubu/breakdancer/perl/bam2cfg.pl] samtools pid process 27629 is still there...
/marcoubu/breakdancer/perl/bam2cfg.pl] invoking kill -9 on 27629 ...
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing samtools process : 27629
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Processing bam: actual_breakdancer_options
[E::hts_open_format] Failed to open file actual_breakdancer_options
samtools view: failed to open "actual_breakdancer_options" for reading: No such file or directory
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing BAM file
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Send TERM signal for 27632
/home/marcoubu/breakdancer/perl/bam2cfg.pl] samtools pid process 27632 is still there...
/home/marcoubu/breakdancer/perl/bam2cfg.pl] invoking kill -9 on 27632 ...
/home/marcoubu/breakdancer/perl/bam2cfg.pl] Closing samtools process : 27632

....and a simil message I've when I launched

/home/marcoubu/breakdancer/perl/bam2cfg.pl -g -h tumor.bam normal.bam > BRC6.cfg

I don't know if it may help you to know that I find the breakdancer-max folder in:

/home/marcoubu/breakdancer/build/build/src/exe

What am I doing wrong?

Thanks a lot.

ADD REPLYlink modified 4 weeks ago by RamRS27k • written 4 weeks ago by dott.difranco0
2

You should talk to someone near you that understands Linux. You're literally passing "actual_breakdancer_options", and there is no way I can make you understand what I'm trying to convey. It's like I'm telling you "Tell me your actual name" and you're replying with "your actual name". It's starting to get silly now.

I have no idea why you're passing in the S17-530 string, and again, you need someone near you that knows Linux. They'll be able to help you better than anyone over the Internet can.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by RamRS27k

Unfortunately I don't have any friends who know linux. From your experience do you think it is impossible for me to undertake the SV reading of my genome?

ADD REPLYlink written 4 weeks ago by dott.difranco0

SV reading of my genome?

It's your own genome? And you are going to dive into the data when you can't run a very basic command? With all respect, but that's highly irresponsible. You need someone with more experience. You can do whatever the hell you want with your own genome, but what do you aim to find?

ADD REPLYlink written 4 weeks ago by WouterDeCoster44k

By "my genome" I meant the genome I need to test. My professor gave me this task and I should finish it. If you can help me, thank you. Nice day

ADD REPLYlink written 4 weeks ago by dott.difranco0

It will be quite challenging to run command line tools without a basic understanding of how the command line works, or how to read and understand command line documentation. I looked for an online version of breakdancer that doesn't need command line knowledge, but it looks like Galaxy might not have it. I'd encourage you to do some more digging to check for any SV detection tool that has a graphical interface, find someone that knows the command line or learn command line basics.

If your professor gave you this task, they believe you have the skill to do this and they will be open to helping you out now that you're having genuine difficulties.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by RamRS27k

Thanks a lot RamRS. Nice day

ADD REPLYlink written 4 weeks ago by dott.difranco0
1

May be you can change the "bam_files " to your real bam path. like /home/xx/work/xx.bam.

ADD REPLYlink written 5 weeks ago by leeray0015110
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