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The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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Clines module has failed.. cnaseq.cnvhmm.tsv file is empty!! #204

Closed shu2010 closed 8 years ago

shu2010 commented 8 years ago

Dear authors, Why is the cnaseq.cnvhmm.tsv file empty although the cnaseq.cnvhmm file exists? Here is the error message:

ERROR RUNNING COMMAND. Exit code 1 from: /opt/gms/HQO1F136/sw/genome/lib/perl/Genome/Model/Tools/CopyNumber/CnView.pm.R 'All' /opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/clonality/cnvs.hq /opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/cnv/wgs_cnv/cnview/CNView_All/CNView_All_genes.tsv /opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/cnv/wgs_cnv/cnview/CNView_All/cnaseq.cnvhmm.tsv /opt/gms/HQO1F136/db/tgi/cancer-annotation/human/build37-20131010/hg19/ideogram/ChrBandIdeogram.tsv /opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/cnv/wgs_cnv/cnview/CNView_All/ ALL 0 0 jpeg 1>/opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/cnv/wgs_cnv/cnview/CNView_All/CNView.R.stdout 2>/opt/gms/HQO1F136/fs/HQO1F136/info/model_data/bc84890343a540f3a744e4c3cfa79ba2/build7ff96061b5674132819d38009e6fb40c/RA_006/cnv/wgs_cnv/cnview/CNView_All/CNView.R.stderr

Best Shu