Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
1
4
Entering edit mode
3.1 years ago
DareDevil ★ 4.3k

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
GenomicsDBImport GATK trio cohort • 1.8k views
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1
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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.

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1
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+1 There was an empty line at the end. Removing it solved my issue

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2
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3.1 years ago

Does your cohort.sample_map has a first empty line?

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2
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+1 Ya. file has an empty line at the end. It's working after removing the last line

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