CNVnator histogram run for too long

[CottusCNV]

Hello!

It's my first time using CNVnator. After creating the .root file I did the following:
./cnvnator -root file.root -chrom groupI -his 100
to generate a histogram. The program seems to be running fine at the beginning, and give out such output:
Warning in <TUnixSystem::SetDisplay>: DISPLAY not set, setting it to minint-612e653.************
Allocating memory ...
Done.
Calculating histograms with bin size of 100 for 'groupI' ...
Making directory bin_100 ...
Making GC histogram for 'groupI' ...

and then it has been running more than 10 hours without any further respond...

Could someone please tell me where the problem could happen?
Thank you very much!!

[vivek_]

http://seqanswers.com/forums/showthread.php?t=21888

This was my experience with a similar issue.

[CottusCNV]

http://seqanswers.com/forums/showthread.php?t=21888

This was my experience with a similar issue.

Thank you very much! I didn't know there has to be linebreaks in the fasta.

[vivek_]

Yeah its kind of trivial but that's how the software reads the fasta files. If you use the reference from the UCSC download directly, it works perfectly well.

When you get the results please let me know if the MAPQ0 value in the output varies with values other than 1 and -1. I haven't been able to figure this out yet.

[CottusCNV]

Yeah its kind of trivial but that's how the software reads the fasta files. If you use the reference from the UCSC download directly, it works perfectly well.

When you get the results please let me know if the MAPQ0 value in the output varies with values other than 1 and -1. I haven't been able to figure this out yet.

I'll let you know.
And now I'm also trying to use another package for CNV calling, it's a R package called "cn.mops", which seem to be much easier to use. I managed to get some results in one day.

[CottusCNV]

Yeah its kind of trivial but that's how the software reads the fasta files. If you use the reference from the UCSC download directly, it works perfectly well.

When you get the results please let me know if the MAPQ0 value in the output varies with values other than 1 and -1. I haven't been able to figure this out yet.

It's always 1 for me. I don't even have a -1...

[vivek_]

Yeah that was my issue as well with the software. The source code is a little hard to read since it uses quite a bit of root modules as well.

They describe the results in the CNVnator paper by doing a filtering on the Mapq0 value and this is kind of important for de novo CNV detection, which is my interest.

[elisold]

so how did you go about creating line breaks in fast (what does mean anyway)? I'm getting the same error ...its stops from "Making histogram.."

cnvnator -root PT0113-C.7009.45.bam.root -d . -his 100
Allocating memory ...
Done.
Calculating histograms with bin size of 100 for 'Pf3D7_01_v3' ...
Making GC histogram for 'Pf3D7_01_v3' ...

[vivek_]

Line breaks simply means each line in the fasta file is limited to 60 bases. You could just have Bio-Perl module read and print the chromosomes in your fasta file in the proper format.

[elisold]

Thanks, I corrected that. But now I get a Maximum buffer size exceeded! Any idea how to correct it?
Calculating histograms with bin size of 1000 for 'Pf3D7_05_v3' ...
Making GC histogram for 'Pf3D7_05_v3' ...
Maximum buffer size exceeded.

[eleven]

Thanks, I corrected that. But now I get a Maximum buffer size exceeded! Any idea how to correct it?
Calculating histograms with bin size of 1000 for 'Pf3D7_05_v3' ...
Making GC histogram for 'Pf3D7_05_v3' ...
Maximum buffer size exceeded.

Hello, I also encounter this problem, so did you solve it, and I found this error would influence our -genome step.

So if you solved, pelease let me know, thanks a lot!

[Bazinga199122]

Line breaks simply means each line in the fasta file is limited to 60 bases. You could just have Bio-Perl module read and print the chromosomes in your fasta file in the proper format.

Hi, I've met this problem,too. It does not work after doing line-breaking by fold command in bash. Can you help me with that? Thanks in advance!

[Alicia B]

Thanks, I corrected that. But now I get a Maximum buffer size exceeded! Any idea how to correct it?
Calculating histograms with bin size of 1000 for 'Pf3D7_05_v3' ...
Making GC histogram for 'Pf3D7_05_v3' ...
Maximum buffer size exceeded.

Hi! did you ever resolve this issue?
I only just started using cnvnator and am coming across the exact same message. Any advice would be much appreciated!

[SES]

Hi! did you ever resolve this issue?
I only just started using cnvnator and am coming across the exact same message. Any advice would be much appreciated!

Still getting this error with the latest version? I haven't seen this one in particular but it could be that you don't have enough memory for the job. Can you run the commands with a smaller test data set?

[Alicia B]

Still getting this error with the latest version? I haven't seen this one in particular but it could be that you don't have enough memory for the job. Can you run the commands with a smaller test data set?

Hi SES,

Thanks for your advice. You were right I wasn't allocating enough memory to run the job, it's now running smoothly.

Thanks for your help!