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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Problem running CNVnator with draft genome by singularity #258

Open Hai1983 opened 2 years ago

Hai1983 commented 2 years ago

Hi everyone.

+I try to use CNVnator with draft genome by singularity 

          singularity run -B /scratch/ulg/bbasv/daomhai/CNVnotorDocker /scratch/users/d/a/daomhai/CNVnotorDocker/cnvnator-docker_v0.3.3.sif cnvnator -root catfish22a.root -tree catfish_sorted.bam.

+This running created is ok with root.file -rw-r--r-- 1 daomhai daomhai 929981665 Jan 22 00:03 catfish22a.root

+I try to continue with: -his, but it seems to fail. And, I do not see any additional file for this running.

          /cnvnator-docker_v0.3.3.sif cnvnator -root catfish22a.root -fasta Catfish22a.scaffolds.fa -his 100

Allocating memory ... Done.

+And, I try with –stat 100, it is failed too.

     /cnvnator-docker_v0.3.3.sif cnvnator -root catfish22a.root -stat 100 
     Making statistics for scaffold1 ...
     Making statistics for scaffold2 ...
     Making statistics for scaffold3 ...
     ……
    Average RD per bin (1-22) is 75.0986 +- 14.439 (before GC correction)
    Average RD per bin (X,Y)  is 0 +- 0 (before GC correction)
   Correcting counts by GC-content for 'scaffold1' ...
    No histogram with GC content for 'scaffold1' found.
   No correction made.
   ….
   Making statistics for scaffold1 after GC correction ...
   Can't find GC-content histogram for 'scaffold1'.
   Making statistics for scaffold2 after GC correction ...
   Can't find GC-content histogram for 'scaffold2'.
    ….
   Can't find GC-content histogram for 'scaffold26'.
   Average RD per bin (1-22) is 75.0986 +- 14.439 (after GC correction)
    Average RD per bin (X,Y)  is 0 +- 0 (after GC correction)
      …..

+Lastly, I run: -call 100, it is fail.

/cnvnator-docker_v0.3.3.sif cnvnator -root catfish22a.root -call 100
Can't find all histograms for 'scaffold1'.

Please help me to figure out what I am doing wrong ??

Sincerely, Hai

abyzov commented 2 years ago

Hi, not sure what causes the problem but I suspect you may need to gzip fasta files with the ref genome. Milovan, could you comment.

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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978