Svtools classify raising ValueError exception

[yachenhu]

Hi,

I encountered a ValueError exception below:

Traceback (most recent call last): File "/titan/hu_yachen/anaconda2/envs/svtools/bin/svtools", line 11, in sys.exit(main()) File "/titan/hu_yachen/anaconda2/envs/svtools/lib/python2.7/site-packages/svtools/cli.py", line 79, in main sys.exit(args.entry_point(args)) File "/titan/hu_yachen/anaconda2/envs/svtools/lib/python2.7/site-packages/svtools/sv_classifier.py", line 660, in run_from_args args.diag_outfile File "/titan/hu_yachen/anaconda2/envs/svtools/lib/python2.7/site-packages/svtools/sv_classifier.py", line 586, in run_reclassifier [params, het_del_fit, hom_del_fit] = calc_params(training_data, sex_chrom_names) File "/titan/hu_yachen/anaconda2/envs/svtools/lib/python2.7/site-packages/svtools/sv_classifier.py", line 229, in calc_params df.loc[:,'q_low']=df.groupby(['sample', 'svtype', 'GT'])['log2r'].transform(lowQuantile) File "/glusterfs/home/hu_yachen/.local/lib/python2.7/site-packages/pandas/core/groupby/generic.py", line 945, in transform result = concat(results).sort_index() File "/glusterfs/home/hu_yachen/.local/lib/python2.7/site-packages/pandas/core/reshape/concat.py", line 228, in concat copy=copy, sort=sort) File "/glusterfs/home/hu_yachen/.local/lib/python2.7/site-packages/pandas/core/reshape/concat.py", line 262, in init raise ValueError('No objects to concatenate') ValueError: No objects to concatenate

The command line I used is:

zcat results/merged.sv.pruned.vcf.gz | svtools classify -g data/samples/817_sex -a data/references/repeatMasker.recent.lt200millidiv.LINE_SINE_SVA.b37.sorted.bed.gz -m naive_bayes -t results/training.vars.vcf.gz > results/output.nb.vcf && bgzip -c results/output.nb.vcf > results/output.nb.vcf.gz

The merged.sv.pruned.vcf.gz file was generated from the svtyper-sso genotyped file. When I replace with svtyper, it won't complain. Anyone knows how to fix this?

Cheers, Yachen