smoove merge error

[dumicola]

Hi,

When I ran smoove merge, I get the following error. How should I resolve this?

My command is $smoove merge --name merged -f $ref --outdir ./09_smoove $outputdir/*.genotyped.vcf.gz

[smoove] 2025/08/22 10:17:04 starting with version 0.2.8
Usage: smoove --name NAME --fasta FASTA [--exclude EXCLUDE] [--excludechroms EXCLUDECHROMS] [--processes PROCESSES] [--outdir OUTDIR] [--noextrafilters] [--support SUPPORT] [--genotype] [--duphold] [--removepr] BAMS [BAMS ...]
error: missing value for --name
[smoove] 2025/08/22 10:17:04 starting with version 0.2.8
[smoove] 2025/08/22 10:17:04 merging 69 files
[smoove] 2025/08/22 10:17:04 finished sorting 69 files; merge starting.
[smoove] 2025/08/22 10:22:17 Required tag PREND not found. Please ensure you've run lumpy withthe -P option to emit breakpoint probabilities.
2025/08/22 10:22:18 exit status 1

Looking forward to your reply and thank you in advance!

[brentp]

from the message, it seems that your --name argument is not getting propagated to smoove. Can you check that first?

[dumicola]

Hi,

I checked it. The --name argument is not causing the merge error. The actual error in the merge process is:

[smoove] 2025/08/22 23:12:04 starting with version 0.2.8
[smoove] 2025/08/22 23:12:04 merging 69 files
[smoove] 2025/08/22 23:12:04 finished sorting 69 files; merge starting.
[smoove] 2025/08/22 23:17:14 Required tag PREND not found. Please ensure you've run lumpy withthe -P option to emit breakpoint probabilities.
2025/08/22 23:17:15 exit status 1

The command I used when calling was:
$smoove call --outdir $outputdir --name ${sample} --fasta $ref -p 24 --genotype $outputdir/${sample}.RG.bam

Looks like the BAM file is missing the PREND tag, but I don't know how to add this tag.

Thinks!