no suitable codecs found

[ytao0210]

When I use gatk to CombineGVCFs, the following error occurs: "Cannot read file because no suitable codecs found". How can I solve this problem？

[droazen]

@ytao0210 Can you please post your complete CombineGVCFs command line, including input file? The input(s) to this tool should have .g.vcf or .g.vcf.gz extensions. Can you confirm that your input(s) are actually GVCF files?

[boutrys]

Hello,

I have the same problem,

path_input_file=/work/gr-fe/archive/sample_repository/all_exome_gvcfs_hg38/FVH/exomes #patient GVCF path_name_individu=/work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_name.txt path_output=/work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_data.vcf.gz tmp_folder=/scratch/sboutry/logs/combine_gvcf_file nbr_groups=2

Path to database and programs

REF=/work/gr-fe/saadat/Reference_Genome/GRCH38_no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz BCFTOOLS=/work/gr-fe/sboutry/tools/bcftools/install/bin/bcftools export BCFTOOLS_PLUGINS=/work/gr-fe/sboutry/tools/bcftools/bcftools/plugins TABIX=/work/gr-fe/sboutry/tools/tabix/tabix-0.2.6/tabix GATK=/work/gr-fe/sboutry/tools/gatk/gatk-4.2.2.0/gatk

cd ${path_input_file}

${GATK} --java-options "-Xmx180G -XX:ParallelGCThreads=36" CombineGVCFs -R ${REF} --variant ${path_name_individu} -O ${path_output}/patient_data.g.vcf.gz

where all my files are like this

JL0015.g.vcf.gz JL0016.g.vcf.gz JL0017.g.vcf.gz JL0018.g.vcf.gz JL0019.g.vcf.gz JL0020.g.vcf.gz JL0182.g.vcf.gz JL0183.g.vcf.gz JL0184.g.vcf.gz JL0185.g.vcf.gz JL0186.g.vcf.gz JL0234.g.vcf.gz JL0278.g.vcf.gz JL0412.g.vcf.gz JL0417.g.vcf.gz JL0515.g.vcf.gz

A USER ERROR has occurred: Cannot read file:///work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_name.txt because no suitable codecs found

Thanks a lot for any help

Best,

Simon

[boutrys]

I just rename the file patient_name.txt patient_name.gvcfs.list

And it worked, in case that can help some