Caused by:
Process `CMGG_CMGGGERMLINE:CMGGGERMLINE:ADD_PED_HEADER:RTGTOOLS_PEDFILTER (Proband)` terminated with an error exit status (1)
Command executed:
rtg pedfilter \
--vcf \
Proband.samples.tsv \
| rtg bgzip - > Proband.vcf.gz
cat <<-END_VERSIONS > versions.yml
"CMGG_CMGGGERMLINE:CMGGGERMLINE:ADD_PED_HEADER:RTGTOOLS_PEDFILTER":
rtgtools: $(echo $(rtg version | head -n 1 | awk '{print $4}'))
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
Error: Conflicting PED definitions of sex for individual -9