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error in vcf2adam #899
When I try to convert vcf to adam, no matter output gzipped or not.
adam-submit vcf2adam test.vcf test_vcf.adam -parquet_compression_codec GZIP
It always gives the following warnings.
Dec 22, 2015 2:28:27 PM WARNING: org.apache.parquet.hadoop.ParquetOutputCommitter: could not write summary file for test_vcf.adam
Also, when i load in test_vcf.adam adam-shell. it always give error:
java.lang.IllegalArgumentException: unknown VCF format, cannot create RecordReader: file:test_vcf.adam/part-r-00000.gz.parquet
I am using the newest adam-0.18.2 with spark-1.5.1-hadoop-2.4 in java 8 environment
Hello! I haven't been able to reproduce those exact warnings. Is the file
Guessing at your input data, note that VCF files representing dbSNP may not include any genotypes, only variants, so you may wish to use the