Closed caot closed 6 years ago
I think that is due to empty input provided, for example demuxlet --help
does not produce that error.
You need to provide VCF as genotypes, as well as SAM/BAM file name
On Wed, May 9, 2018, 11:20 PM Cao T notifications@github.com wrote:
What might be the reason on the followins issue of FATAL ERROR:
$ which demuxlet /path-to/demuxlet-20180509/bin/centos/demuxlet $ demuxlet
Available Options
The following parameters are available. Ones with "[]" are in effect: Options for input SAM/BAM/CRAM : --sam, --tag-group [CB], --tag-UMI [UB] Options for input VCF/BCF : --vcf, --field [GP], --geno-error [0.01], --min-mac [1], --min-callrate [0.50], --sm, --sm-list Output Options : --out, --alpha, --write-pair, --doublet-prior [0.50], --sam-verbose [1000000], --vcf-verbose [10000] Read filtering Options : --cap-BQ [40], --min-BQ [13], --min-MQ [20], --min-TD, --excl-flag [3844] Cell/droplet filtering options : --group-list, --min-total, --min-uniq, --min-snp
Run with --help for more detailed help messages of each argument.
FATAL ERROR - [bcf_filtered_reader.cpp:5 void BCFFilteredReader::init_params()] bcf_file_name is empty
terminate called after throwing an instance of 'pException' what(): Exception was thrown Aborted
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What might be the reason on the followins issue of FATAL ERROR: