Comments (4)
It seems like the CNVnator binary is not finding the ROOT libraries. Are you sourcing the ROOT file prior to running speedseq? It's best to have something like the following in the speedseq.config file:
source /gsc/pkg/root/root/bin/thisroot.sh
Then just run cnvnator-multi to make sure it's working properly before running speedseq:
$ /opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/cnvnator-multi
Not enough parameters.
CNVnator v0.3
Usage:
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root out.root [-genome name] [-chrom 1 2 ...] -tree file1.bam ...
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root out.root [-genome name] [-chrom 1 2 ...] [-nthreads threads] -ptree file1.bam ...
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root out.root [-genome name] [-chrom 1 2 ...] -merge file1.root ...
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root [-genome name] [-chrom 1 2 ...] [-d dir] -his bin_size
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root [-chrom 1 2 ...] -stat bin_size
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root -eval bin_size
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root [-chrom 1 2 ...] -partition bin_size [-ngc]
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root [-chrom 1 2 ...] -call bin_size [-ngc]
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root -genotype bin_size [-ngc]
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -root file.root -view bin_size [-ngc]
/gscmnt/gc2719/halllab/users/cchiang/src/speedseq/bin/cnvnator-multi -pe file1.bam ... -qual val(20) -over val(0.8) [-f file]
Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19
from speedseq.
Ah yes, I can see the path to thisroot.sh
isn't setup correctly.
I'll have to get our syadmin to sort it. Will update you in due course once it's fixed to confirm this was indeed the issue.
Thanks for the help. :)
from speedseq.
Our sysadmin has managed to rectify it; I get the correct usage when running /opt/gridware/pkg/apps/speedseq/0.0.3a/gcc-4.4.6+root-5.34.30+samtools-0.1.19+python-2.7.3/bin/cnvnator-multi
.
However, now I'm back with the same problem as #40. Could you reopen that one? I'll add some more info to it rather than this one for clarity.
from speedseq.
ok, good I;m closing this and reopening the other issue
from speedseq.
Related Issues (20)
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- Error -running speedseq SV - missing pair end parameters:mean stdev
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- Linker error when doing `make cnvnator`
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- Bam file not generated using speedseq align
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- configure: error: cannot guess build type; you must specify one
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- make :can not find -lCore -lRIO -lHist -lGraf -lGpad -lTree -lMathCore
- Are CRAM files supported by SpeedSeq?
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from speedseq.