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Published 20 hours ago • verified publisher icon hall-lab

Issue with CNVnator installation

Open ragans opened this issue 9 years ago • 2 comments

I am having an issue identical to the closed issue #28 . I have sourced the root installation and tired the suggestion from the seqanswers link you found (http://seqanswers.com/forums/showthread.php?t=16665).

When we run the make cnvnator-multi we are getting the error: g++ -m64 -O3 -DCNVNATOR_VERSION="v0.3" -I/net/gs/vol3/software/modules-sw/ROOT/5.34.14/Linux/RHEL6/x86_64/include -Isrc/samtools -c src/cnvnator.cpp -o src/obj/cnvnator.o In file included from src/cnvnator.cpp:8: src/HisMaker.hh:11:20: error: TFrame.h: No such file or directory

I'm wondering if it may be related to the version of Root we are using (5.34.14) or if that matters.

Otherwise, the speedseq installation is working and we can run the speedseq sv without the "-d" flag.

Also, other than reading about the impact on sensitivity and FDR in the Lumpy paper, I don't have a full understanding of how the read depth is utilized by Lumpy the the impact on the output. I'm sure there is a line in the README or something I have missed - could you point me to the best spot for that?

Thanks very much for your support and work on this software.

Kind regards, Seamus Ragan

ragans avatar Sep 02 '15 23:09 ragans

I don't have much experience with different versions of ROOT, but we're using v5.34.20 on our system so I can confirm it works with that. I don't have any ideas for the TFrame error other than those mentioned in the seqanswers thread, but I would attempt to install the standard version of CNVnator first to simplify troubleshooting. If your ROOT install cooperates with the standard CNVnator then it should also work with SpeedSeq's version.

SpeedSeq primarily uses CNVnator to annotate the read-depth of variants that were discovered by LUMPY. This adds a "CN" field to the genotypes of each sample in the VCF. It also produces a separate BED file with the suffix ".sv.readdepth.bed" with the copy number intervals produced by CNVnator.

cc2qe avatar Sep 03 '15 12:09 cc2qe

colby, Thanks very much for the details. I'll continue to work with our admins to try to get the build right.

It's fine to close this issue.

Thanks again for your help and the quick response.

Kind regards, Seamus Ragan

ragans avatar Sep 03 '15 18:09 ragans