Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
I used following command GenomicsDBImport from GATK (version 4.1.4.1)
gatk GenomicsDBImport \
--sample-name-map cohort.sample_map \
--batch-size 50 --reader-threads 12 \
--genomicsdb-workspace-path trio_db \
--intervals targetR.interval_list
The content of cohort.sample_map is as follows:
XX1C1 XX1C1_genome_int.vcf.gz
XX1c2 XX1c2_genome_int.vcf.gz
XX1P1 XX1P1_genome_int.vcf.gz
XX1P2 XX1P2_genome_int.vcf.gz
XX3C XX3C_genome_int.vcf.gz
XX3P1 XX3P1_genome_int.vcf.gz
XX3P2 XX3P2_genome_int.vcf.gz
XX4C XX4C_genome_int.vcf.gz
XX4P1 XX4P1_genome_int.vcf.gz
XX4P2 XX4P2_genome_int.vcf.gz
I got following error while running the command
A USER ERROR has occurred: Bad input: Expected a file with 2 fields per line in the format
Sample File
but found line: "" with 1 fields
1 answer
Does your cohort.sample_map has a first empty line?
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Check if the separator is tab or a series of white spaces. If it's the latter, replace it with tab. That might work.
+1 There was an empty line at the end. Removing it solved my issue