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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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std::logic_error when running Basic Command #305

Open cantlap opened 8 months ago

cantlap commented 8 months ago

I am getting the following error message when I try to run this command:

singularity run docker://ghcr.io/dnanexus-rnd/glnexus:v1.4.1 glnexus_cli -d {outdir} -c DeepVariant_unfiltered --list {bam file list}

INFO: Using cached SIF image INFO: underlay of /etc/localtime required more than 50 (77) bind mounts [339884] [2024-01-30 12:49:16.486] [GLnexus] [info] glnexus_cli release v1.4.1-0-g68e25e5 Aug 13 2021 [339884] [2024-01-30 12:49:16.488] [GLnexus] [info] detected jemalloc 5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756 terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid Aborted (core dumped)

bijinpeng commented 1 month ago

do not used the -d parameter may fill this error