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Is CNVnator a software that can only run in single-thread mode? #281
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Hi,
by default CNVnator is compiled with OMP parallel support. During segmentation step it can use as many core as provided.
Alexej Abyzov, Ph.D.
Senior Associate Consultant,
Associate Professor of Biomedical Informatics,
Department of Quantitative Health Sciences,
Center for Individualized Medicine, Mayo Clinic
-----------------------------
Mayo Clinic, 200 1st street SW, Harwick 7-91
Rochester, MN 55905
www.abyzovlab.org
tel: +1-(507)-538-0978
|
Sorry for forgetting to reply, thank you, I have solved it, just need to add "export OMP_NUM_THREADS=number" to solve it. |
In addition, I have a sample, I have run it many times, but it has been unable to run the result, can you help me to see why? CommandCNVnator_input=/xxx/xxx.marked.realigned.recal.bam LogError in TBasket::Create: Cannot allocate 14069 bytes for ID = position Title = chr2 |
Hi,
Is it the only sample that fails?
When working with BAM you don’t need to specify genome.
Alexej Abyzov, Ph.D.
Senior Associate Consultant,
Associate Professor of Biomedical Informatics,
Department of Health Sciences Research,
Center for Individualized Medicine, Mayo Clinic
-----------------------------
Mayo Clinic, 200 1st street SW, Harwick 3-12
Rochester, MN 55905
www.abyzovlab.org<http://www.abyzovlab.org/>
tel: +1-(507)-538-0978<tel:+15075380978>
|
No, there were a dozen of them. Yes, I later learned that if I use bam I don't need to specify the genome, but it ignores the --genome parameter. This bam like: |
Another problem is that I see someone filtering the vcf results of CNVnator with the following conditions: "CNV calls were filtered using stringent criteria including P-value < 0.05 and minimum size > 1 Kb, and calls with > 50% of q0 (zero mapping quality) reads within the CNV regions were removed (q0 filter). " minimum size can be filtered using the SVLEN key. example: |
Error"File is more than 2 Gigabytes" such as: |
Hi,
file size shouldn’t be a problem. I worked with files that were over 3 Gb and had no issues.
What is the size of the files you are working with? Looks like in Tb range. Is it correct?
Alexej Abyzov, Ph.D.
Senior Associate Consultant,
Associate Professor of Biomedical Informatics,
Department of Health Sciences Research,
Center for Individualized Medicine, Mayo Clinic
-----------------------------
Mayo Clinic, 200 1st street SW, Harwick 7-91
Rochester, MN 55905
www.abyzovlab.org
<http://www.abyzovlab.org>tel: +1-(507)-538-0978
|
Hi, Error logParsing file /xxx/sample.marked.realigned.recal.bam ... real 49m47.400s real 0m0.062s Anyway, I've solved the problem (splitting into single chromosomes), thanks for your reply. If someone is having the same problem as me, hopefully this solution will help them. |
Good hear. Thanks for letting us know.
Alexej Abyzov, Ph.D.
Senior Associate Consultant,
Associate Professor of Biomedical Informatics,
Department of Quantitative Health Sciences,
Center for Individualized Medicine, Mayo Clinic
-----------------------------
Mayo Clinic, 200 1st street SW, Harwick 7-91
Rochester, MN 55905
www.abyzovlab.org
<http://www.abyzovlab.org>tel: +1-(507)-538-0978
|
Is CNVnator a software that can only run in single-thread mode? Is CNVnator a software that can only run in single-thread mode?
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