Igor Trujnara
03/18/2026, 8:26 AMError 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?