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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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No chromosome/contig information parsed. #247

Open lxingze opened 3 years ago

lxingze commented 3 years ago

Dear author It's running successfully: 2.1 EXTRACTING READ MAPPING FROM BAM/SAM FILES

But when I ran 2.2, it got the following error $ cnvnator -root file.root -his 1000 -d genome.fasta

Calculating histograms with bin size of 1000 for 'Chr11' ... Making GC histogram for 'Chr11' ... Can't open file with chromosome sequence. No chromosome/contig information parsed. Sequence length (0) is different from expectation (81578583) for 'Chr11'. Doing nothing! Done.

Hope to get your answer !!!

abyzov commented 3 years ago

Hi, for some reason the tool can’t parse genome from the fasta file provided. What is the header in the file?

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

lxingze commented 3 years ago

The FASTA file name is genome.fa The titles are chr1, Chr2,..., Chr11

abyzov commented 3 years ago

Hi, is there a small chromosome that you can take its sequencing and send to me (zipped) to debug?

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

abyzov commented 3 years ago

Hi, could you share a sample file with us somehow?

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

wjtmms commented 2 years ago

Dear author

I have encountered the same problem as the aforementioned, but I couldn't find the solution. image

how can I solve this problem?