Hello, I have found a new error, this time it look...
# sarek
i
Hello, I have found a new error, this time it looks more normal, but I have no idea what went wrong
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Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES (SRX8569566)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES (SRX8569566)` terminated with an error exit status (134)


Command executed:

  freebayes \
      -f GCF_036512215.1_SLM_r2.1_genomic.fna.gz \
      --target NC_090802.1_1-68736248.bed \
       \
       \
       \
      --min-alternate-fraction 0.1 --min-mapping-quality 1 \
      SRX8569566.md.cram > SRX8569566.NC_090802.1_1-68736248.vcf
  
  bgzip SRX8569566.NC_090802.1_1-68736248.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES":
      freebayes: $(echo $(freebayes --version 2>&1) | sed 's/version: *v//g' )
  END_VERSIONS

Command exit status:
  134

Command output:
  (empty)

Command error:
  [E::bgzf_index_load] Error opening GCF_036512215.1_SLM_r2.1_genomic.fna.gz.gzi : No such file or directory
  [E::bgzf_open_ref] Unable to load .gzi index 'GCF_036512215.1_SLM_r2.1_genomic.fna.gz.gzi'
  [E::refs_load_fai] Failed to open reference file 'GCF_036512215.1_SLM_r2.1_genomic.fna.gz'
  terminate called after throwing an instance of 'std::invalid_argument'
    what():  Could not read reference genome GCF_036512215.1_SLM_r2.1_genomic.fna.gz for CRAM opt
  .command.sh: line 9: 1758361 Aborted                 (core dumped) freebayes -f GCF_036512215.1_SLM_r2.1_genomic.fna.gz --target NC_090802.1_1-68736248.bed --min-alternate-fraction 0.1 --min-mapping-quality 1 SRX8569566.md.cram > SRX8569566.NC_090802.1_1-68736248.vcf
Has anyone seen this before?