search

statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
117 stars 25 forks source link

FATAL ERROR - [bcf_filtered_reader.cpp:5 void BCFFilteredReader::init_params()] bcf_file_name is empty #24

Closed caot closed 6 years ago

caot commented 6 years ago

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
jpfairbanks commented 6 years ago

I think that is due to empty input provided, for example demuxlet --help does not produce that error.

hyunminkang commented 6 years ago

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/24, or mute the thread https://github.com/notifications/unsubscribe-auth/AF-OuYYja1VxUL6uX_ES4qAEdMSmd2L9ks5twvsNgaJpZM4T4aDD .