Closed loipf closed 3 years ago
In the GVCF files, the sample ID needs to be set to a unique identifier. Currently they all seem to be set to "default" (from your zip):
(rightmost of the third line)
You can rewrite the headers pretty efficiently using bcftools reheader
but better would be to adjust the upstream pipeline to put the sample IDs there in the first place. DeepVariant might be filling it from the SAM/BAM/CRAM file header (RG SM:default
?) which in turn was an input to the read aligner (I'm not certain of that though).
this solved the problem! thank you very much for the detailed answer, also with the reheader info
hi,
similar to https://github.com/dnanexus-rnd/GLnexus/issues/241 , I get the same error. However, after I check the gvcf file, it seems to me that my sample ID is unique enough, and i wondered whether there is any other possibility for this condition.
Part of my error report in log file is shown as follows: [85597] [2022-03-09 13:57:34.574] [GLnexus] [info] config CRC32C = 3285998180 [85597] [2022-03-09 13:57:34.574] [GLnexus] [info] init database, exemplar_vcf=/input/DD19003942_C_WES.g.vcf.gz [85597] [2022-03-09 13:57:34.932] [GLnexus] [info] Initialized GLnexus database in GLnexus.DB [85597] [2022-03-09 13:57:34.932] [GLnexus] [info] bucket size: 30000 [85597] [2022-03-09 13:57:34.932] [GLnexus] [info] contigs: chr1 chr2 chr3 chr4 ..... [85597] [2022-03-09 13:57:34.960] [GLnexus] [info] db_get_contigs GLnexus.DB [85597] [2022-03-09 13:57:35.195] [GLnexus] [info] Beginning bulk load with no range filter. [E::hts_open_format] Failed to open file /intput/DD19003942_M_WES.g.vcf.gz [E::hts_open_format] Failed to open file /intput/DD19003942_F_WES.g.vcf.gz [85597] [2022-03-09 13:57:55.301] [GLnexus] [info] Loaded 1 datasets with 1 samples; 970692232 bytes in 11262072 BCF records (4 duplicate) in 97672 buckets. Bucket max 365608 bytes, 3915 records. 0 BCF records skipped due to caller-specific exceptions [85597] [2022-03-09 13:57:55.303] [GLnexus] [info] Created sample set *@1 [85597] [2022-03-09 13:57:55.303] [GLnexus] [error] /intput/DD19003942_F_WES.g.vcf.gz IOError: opening gVCF file (/intput/DD19003942_F_WES.g.vcf.gz) [85597] [2022-03-09 13:57:55.304] [GLnexus] [error] /intput/DD19003942_M_WES.g.vcf.gz IOError: opening gVCF file (/intput/DD19003942_M_WES.g.vcf.gz) [85597] [2022-03-09 13:57:59.318] [GLnexus] [error] Failed to bulk load into DB: Failure: One or more gVCF inputs failed validation or database loading; check log for details. Failed to read from standard input: unknown file type
hi,
similar to #232 , I get the same error, but while I am using the latest docker image. the .vcf files are created with Deepvariant 1.0.0 and I am using the image
quay.io/mlin/glnexus:v1.2.7
the "getting started" example works perfectly in the image. the only difference is I am reading the files from separate folders but this should not matter.the 3 small example vcf files used (on MT chrom): error_vcf.zip
the (default) command used:
please ask if you need additional information, thank you for your help
the error: