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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Can't find directory 'bin_1000'. Can't find RD histogram for 'chr1'. #252

Open liuhankui opened 2 years ago

liuhankui commented 2 years ago

/anaconda3/envs/myenv/bin/cnvnator -root B.root -chrom chr1 -tree chr1.bam /anaconda3/envs/myenv/bin/cnvnator -root B.root -his 1000 -fasta ucsc.hg19.fasta -chrom chr1 /anaconda3/envs/myenv/bin/cnvnator -root B.root -stat 1000 -chrom chr1 /anaconda3/envs/myenv/bin/cnvnator -root B.root -partition 1000 -ngc /anaconda3/envs/myenv/bin/cnvnator -root B.root -call 1000 -ngc

stand output is： Parsing file chr1.bam ... Allocating memory ... Done. Filling and saving tree for 'chr1' ... Writing histograms ... Total of 15468573 reads were placed. Allocating memory ... Done. Making statistics for chr1 ... Average RD per bin (1-22) is 0 +- 0 (before GC correction) Average RD per bin (X,Y) is 0 +- 0 (before GC correction) Making directory bin_1000 ... Correcting counts by GC-content for 'chr1' ... Making statistics for chr1 after GC correction ... Average RD per bin (1-22) is 0 +- 0 (after GC correction) Average RD per bin (X,Y) is 0 +- 0 (after GC correction)

error output is： Can't find directory 'bin_1000'. Can't find directory 'bin_1000'. Can't find directory 'bin_1000'. Can't find directory 'bin_1000'. Can't find RD histogram for 'chr1'. Can't find unique RD histogram for 'chr1'. Can't find histogram for 'chr1'. Can't find any histograms. Can't find any histograms.

once I output the root file into a new file /anaconda3/envs/myenv/bin/cnvnator -root B.root -his 1000 -fasta ucsc.hg19.fasta -outroot his.root the size of his.root file is only 395， but the size of B.root file is 22M

the version of cnvnator from conda is v0.4.1

abyzov commented 2 years ago

Hi, not sure when you need to copy A.root to B.root. How was A.root generated?

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

liuhankui commented 2 years ago

Hi, not sure when you need to copy A.root to B.root. How was A.root generated? 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.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978

Oh, Copy A.root to B.root is not necessary. I do it for saving the time of the first step. please find the pipeline here: /anaconda3/envs/myenv/bin/cnvnator -root B.root -chrom chr1 -tree chr1.bam /anaconda3/envs/myenv/bin/cnvnator -root B.root -his 1000 -fasta ucsc.hg19.fasta -chrom chr1 /anaconda3/envs/myenv/bin/cnvnator -root B.root -stat 1000 -chrom chr1 /anaconda3/envs/myenv/bin/cnvnator -root B.root -partition 1000 -ngc /anaconda3/envs/myenv/bin/cnvnator -root B.root -call 1000 -ngc

abyzov commented 2 years ago

Don’t have idea at the moment. What is the file size before and after -his step?

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

liuhankui commented 2 years ago

Don’t have idea at the moment. What is the file size before and after -his step? 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.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978

There is no change in file size A.root is the file before -his step B.root is the file after -his step

Although the file size has no change, my computer takes 2 hours to finish -his step

image

liuhankui commented 2 years ago

Don’t have idea at the moment. What is the file size before and after -his step? 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.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978

I use cnvpytor for the same bam file, cnvpytor works.

suvakov commented 2 years ago

What is output of command: /anaconda3/envs/myenv/bin/cnvnator -root B.root -ls

If you can share root file, please send me on email (my email is suvakov at gmail) to check. Thanks.

huangl07 commented 1 year ago

is there any solution?

Duanyaoyuan commented 1 year ago

I had this problem too, executing the code

cnvnator -root a.root -his 1000 -chrom $(seq -f 'chr%g' 1 9) chrUn -fasta /home/genome/swo_v4/Csiv4.chromosome.fa

cnvnator -root a.root -stat 1000

Then report an error

Can't find directory 'bin_1000'

This is how I solved it. There are multiple FA files under my swo_v4 file. I re -created one of the only csiv4.chromosome.fa folders and stored this file in. This problem solved this problem.

cnvnator -root ./1.root/${i}.root -his 1000 -d "/sowv4_cnv/"

希望帮助到，poor English

vegetableyu commented 8 months ago

I had this problem too, executing the code

cnvnator -root a.root -his 1000 -chrom $(seq -f 'chr%g' 1 9) chrUn -fasta /home/genome/swo_v4/Csiv4.chromosome.fa

cnvnator -root a.root -stat 1000

Then report an error

Can't find directory 'bin_1000'

This is how I solved it. There are multiple FA files under my swo_v4 file. I re -created one of the only csiv4.chromosome.fa folders and stored this file in. This problem solved this problem.

cnvnator -root ./1.root/${i}.root -his 1000 -d "/sowv4_cnv/"

希望帮助到，poor English

Hi, I had the same problem, the process was: cnvnator -root ${ID}.root -tree ${BAM} cnvnator -root ${ID}.root -his ${BIN_SIZE} -chrom ${CHRlist} -fasta ${USER_REF} cnvnator -root ${ID}.root -stat ${BIN_SIZE} Then report: Can't find directory 'bin_100'. I wonder how you solved it, do you mean putting ${USER_REF} in a separate folder? Could you elaborate on that? Thanks for your time! yu

abyzov commented 7 months ago

Hello, for some reason histograms were not created. Were there any specific messages when executing -his step?

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.orgtel: +1-(507)-538-0978

vegetableyu commented 7 months ago

Hello, for some reason histograms were not created. Were there any specific messages when executing -his step? 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.orgtel: +1-(507)-538-0978

Thanks for reply, the issue has been resolved. The sequence tagging of FASTA should have information of sequence length, otherwise it will cause this error.