Hi all I get this error but I believe the index already is available

A USER ERROR has occurred: An index is required but was not found for file Homo_sapiens_assembly38.dbsnp.vcf.gz. Support for unindexed block-compressed files has

been temporarily disabled. Try running IndexFeatureFile on the input.

This is my code nextflow r`un nf-core/sarek \`

--input annotation.csv \

--outdir mapping1 \

--genome GATK.GRCh38 \

--step mapping \

--wes true \

--intervals Focus_GRCh38.bed \

--skip_tools markduplicates \

--known_indels /flask/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz \

--dbsnp /flask/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.dbsnp.vcf.gz \

--save_output_as_bam true \

--save_mapped true \

--trim_fastq true \

-profile crick \

-r 3.4.2 \

-resume

Please look both the files and indexed are in the same folder

ls /flask/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta

Homo_sapiens_assembly38.dbsnp138.vcf.gz   Homo_sapiens_assembly38.known_indels.vcf.gz         NISTIntegratedCalls.hg38.vcf.gz

Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi Homo_sapiens_assembly38.known_indels.vcf.gz.tbi       NISTIntegratedCalls.hg38.vcf.gz.tbi

Homo_sapiens_assembly38.dbsnp.vcf.gz     Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz

Homo_sapiens_assembly38.dbsnp.vcf.gz.tbi   Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz.tbi

Thanks a lot for any help

Hi, @mina ming! Slack uses channels to organise discussions. Press the

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more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Rike Hanssen for help.

But to answer your question: you are setting `--known_indels /flask/reference/Genomics/aws-igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz`` but the

genome

flag still loads the index for the default

known_indels

. Yes i know that that is bad and we need to either fail the pipeline or at the very least print a giant warning. but until then: if you have the index set

--known_indels_tbi <path/to/index>

if you don't have the index:

--known_indels_tbi false

this will then compute it

A massive thanks because no where in Google you can find this

Hi, @mina ming! Slack uses channels to organise discussions. Press the

...

more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @mina ming for help.