Issue with eval target

[ArjenB85]

I am trying to run the pipeline on some targeted amplicon sequencing by using the recommended settings (by using eval as target eval and providing a .bed file).

The pipeline runs fine if I use
snakemake call -p -j1 --configfile config.yml
or
snakemake qc -p -j1 --configfile config.yml

But if I run snakemake eval -p -j1 --configfile config.yml

It gives this error:

zcat 1L/sv_calls/1L_cutesv_filtered.vcf.gz | sed 's/SVTYPE=DUP/SVTYPE=INS/g' | bcftools view -i '(SVTYPE = "INS" || SVTYPE = "DEL")' | bgziptabix 1L/sv_calls/1L_cutesv_filtered_eval.vcf.gz
[E::vcf_hdr_read] No sample line
Failed to read from standard input: could not parse header
[Mon May 17 13:02:32 2021]
Error in rule eval_reformat:
jobid: 2
output: 1L/sv_calls/1L_cutesv_filtered_eval.vcf.gz
shell:
zcat 1L/sv_calls/1L_cutesv_filtered.vcf.gz | sed 's/SVTYPE=DUP/SVTYPE=INS/g' | bcftools view -i '(SVTYPE = "INS" || SVTYPE = "DEL")' | bgziptabix 1L/sv_calls/1L_cutesv_filtered_eval.vcf.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job eval_reformat since they might be corrupted:
1L/sv_calls/1L_cutesv_filtered_eval.vcf.gz
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/Prairie_Vole_Data/Arjen_Folder/Arjen/pipeline-structural-variation-2.0.2/.snakemake/log/2021-05-17T130127.190721.snakemake.log

I checked the filtered .vcf file and indeed there is no header. Not sure why this is happening. If I run eval on the test samples it works fine.

Help is much appreciated!
Arjen

[ArjenB85]

Actually if I run snakemake -p -j1 --configfile config.yml
the resulting filtered.vcf does not have a proper header either. I am very curious what the problem could be!