Hello! I’m using sarek v3.7.1 to to somatic variant calling and I running into this error where the index file is newer than the vcf file. I’m wondering if anyone has any idea about this error! -[nf-core/sarek] Pipeline completed with errors- WARN: Killing running tasks (85) ERROR ~ Error executing process > ‘NFCORE_SAREKsarekBAM_VARIANT_CALLING_SOMATIC_ALLBAM VARIANT CALLING FREEBAYESVCFLIB_VCFFILTER (RABCA_A71_TUR_vs_RABCA_A71_RC-Nodes)’ Caused by: Process

NFCORE_SAREK:sarek:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:VCFLIB_VCFFILTER (RABCA_A71_TUR_vs_RABCA_A71_RC-Nodes)

terminated with an error exit status (1) Command executed: vcffilter \ --info-filter ‘QUAL > 30’ \ RABCA_A71_TUR_vs_RABCA_A71_RC-Nodes.freebayes.vcf.gz \ | bgzip -c > RABCA_A71_TUR_vs_RABCA_A71_RC-Nodes.freebayes.filtered.vcf.gz cat <<-END_VERSIONS > versions.yml “NFCORE_SAREKsarekBAM_VARIANT_CALLING_SOMATIC_ALLBAM VARIANT CALLING FREEBAYESVCFLIB_VCFFILTER”: vcflib: 1.0.14 END_VERSIONS Command exit status: 1 Command output: (empty) Command error: bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) [tabix++] the index file is older than the vcf file. Please use ‘-f’ to overwrite or reindex.

The reason is likely that you are on a cluster where some nodes have (slightly) different clock settings than others, and if a file is created on one node and the index on another, the time stamp of the index can appear older than the file. Other software packages just issue a warning for that, but

vcftools

apparently requires an extra parameter to stay alive. You have two choices -- just try again (with

-resume

) and hope for better luck, or write a custom config where you add

-f

to whatever

VCFLIB_VCFFILTER

uses as

ext.args

. The first one takes less effort, so I would try that first. You can also bring this up with your sysadmins, maybe they can sync the clocks. If it happens all the time, I would move to the custom config.