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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Failed stat step #167

Closed asmariyaz23 closed 3 years ago

asmariyaz23 commented 5 years ago

Hello,

I am running CNVnator in the following manner:

Extracting reads

cnvnator -root ./file.root -tree 0480_001.sorted.dup.recal.final.bam -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y
Parsing file 0480_001.sorted.dup.recal.final.bam ...
Allocating memory ...
Done.
Filling and saving tree for '1' ...
Filling and saving tree for '2' ...
Filling and saving tree for '3' ...
Filling and saving tree for '4' ...
Filling and saving tree for '5' ...
Filling and saving tree for '6' ...
Filling and saving tree for '7' ...
Filling and saving tree for '8' ...
Filling and saving tree for '9' ...
Filling and saving tree for '10' ...
Filling and saving tree for '11' ...
Filling and saving tree for '12' ...
Filling and saving tree for '13' ...
Filling and saving tree for '14' ...
Filling and saving tree for '15' ...
Filling and saving tree for '16' ...
Filling and saving tree for '17' ...
Filling and saving tree for '18' ...
Filling and saving tree for '19' ...
Filling and saving tree for '20' ...
Filling and saving tree for '21' ...
Filling and saving tree for '22' ...
Filling and saving tree for 'X' ...
Filling and saving tree for 'Y' ...
Writing histograms ... 
Total of 682966990 reads were placed.

Histogram

cnvnator -root file.root -his 1000 -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y -fasta genome.fa.gz 
Allocating memory ...
Done.

Stats

cnvnator -root file.root -stat 1000
Can't find directory 'bin_1000' in file '/scratch/wgs/cnv/CNVnator/file.root'.

I would like to call CNVs later on. Is there something wrong with the histogram step?

Thank you, Asma

suvakov commented 5 years ago

Can you list chromosomes in genome.fa.gz? You can use zgrep: zgrep "^>" genome.fa.gz or samtools: samtools faidx genome.fa.gz cat genome.fa.gz.fai

asmariyaz23 commented 5 years ago

zgrep "^>" genome.fa.gz

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT

abyzov commented 5 years ago

Hi, is it all output that you get from -his step. If so, then something went wrong during making histograms. You should get output something like

Allocating memory ... Done. Calculating histograms with bin size of 200 for 'chr1' ... Making GC histogram for 'chr1' ... Done.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant 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.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745