Can pepper be used for short contigs?

[zhan4429]

I am the system admin for HPC. I just deployed pepper to our cluster based on singularity container. I ran pepper with your test datasets, and did not notice any issue. However, one user said she got issues running it. I noticed that her fasta reference is a short sequence (~1KB). From the her running log, I found no configs or vcfs are found:

CONTIGS FOUND IN PEPPER VCF:
[01-18-2024 11:17:07] INFO: [4/9] RUNNING THE FOLLOWING COMMAND

time margin phase /cluster/home/yzhang85/Pepper_heidi/barcode02.align.sort.bam /cluster/home/yzhang85/Pepper_heidi/MVser_cons.fasta /cluster/home/yzhang85/Pepper_heidi/barcode02_pepper_output/intermediate_files/PEPPER_VARIANT_FULL.vcf.gz /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json -t 4 -V -o /cluster/home/yzhang85/Pepper_heidi/barcode02_pepper_output/intermediate_files/PHASED.PEPPER_MARGIN 2>&1 | tee /cluster/home/yzhang85/Pepper_heidi/barcode02_pepper_output/logs/2_margin_haplotag.log;
samtools index -@4 /cluster/home/yzhang85/Pepper_heidi/barcode02_pepper_output/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam

Running OpenMP with 4 threads.
> Parsing model parameters from file: /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json
> Parsed 0 total VCF entries from /cluster/home/yzhang85/Pepper_heidi/barcode02_pepper_output/intermediate_files/PEPPER_VARIANT_FULL.vcf.gz; kept 0 HETs, skipped 0 for region, 0 for not being PASS, 0 for being homozygous, 0 for being INDEL
No valid VCF entries found!

I am wondering whether this is because pepper cannot be used in short configs.

Best,
Yucheng