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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Calculating histograms error #12

Closed biozzq closed 9 years ago

biozzq commented 9 years ago

Deal all, Very popular tool to call CNVs. For me, an error bothers me for a long time when running calculating histograms. My commands like following,

cnvnator -unique -root output.root -tree test.sort.dedup.realn.bam (succeed) cnvnator -root ouput.root -his 200 -d /ref/sep/ (failed)

and the error logs

Total of 1534005368 reads were placed. Allocating memory ... Done. Calculating histograms with bin size of 200 for '1' ... Making directory bin_200 ... Making GC histogram for '1' ... SysError in TFile::Seek: cannot seek to position -1634381530 in file ERR194147.root, retpos=-1 (Invalid argument) SysError in TFile::Seek: cannot seek to position 8419450657427287862 in file ERR194147.root, retpos=-1 (Invalid argument) Error in TFile::ReadBuffer: error reading all requested bytes from file ERR194147.root, got 8522541 of 67108895 Error in TKey::ReadFile: Failed to read data. SysError in TFile::Seek: cannot seek to position -216073498781733252 in file ERR194147.root, retpos=-1 (Invalid argument) Done.

The version I used is v0.3.2, I hope you can help me, any suggestion will be appreciated.

best wishes.

abyzov commented 9 years ago

Hello, looks like your file got corrupted. Not sure about the reason. If the issue persist, the walk around is to save histograms into a different .root file. e.g.

cnvnator -root tree.root -outroot his.root -his 200 -d /ref/sep/

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, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

biozzq commented 9 years ago

Dear Alexej Abyzov,

Good, it works now according to your suggestion. Thanks.