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cc2qe avatar cc2qe commented on July 28, 2024

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.

s-boardman avatar s-boardman commented on July 28, 2024

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.

s-boardman avatar s-boardman commented on July 28, 2024

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.

cc2qe avatar cc2qe commented on July 28, 2024

ok, good I;m closing this and reopening the other issue

from speedseq.

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