no SQ lines present in the header

To whom it may concern

In the process of using winnowmap, I encountered the following problems. Can you give me some help? thanks！

winnowmap -W repetitive_k9.txt -x map-pb -a -Y -L --eqx --MD --cs -t 60 ../hifi.fasta genome.fasta |samtools view -@ 20 -hb > read_alignment.bam

[M::mm_idx_gen::0.000*72.64] reading downweighted kmers
[M::mm_idx_gen::0.001*5.14] collected downweighted kmers, no. of kmers read=2270
[M::mm_idx_gen::0.001*5.12] saved the kmers in a bloom filter: hash functions=2 and size=32640
[M::mm_idx_gen::188.709*1.04] collected minimizers
[M::mm_idx_gen::202.242*1.07] sorted minimizers
**[WARNING] For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.**
[M::main::202.242*1.07] loaded/built the index for 234214 target sequence(s)
[M::main::202.242*1.07] running winnowmap in SV-aware mode
[M::main::202.242*1.07] stage1-specific parameters minP:1000, incP:1.99, maxP:8000, sample:1000, min-qlen:10000, min-qcov:0.5, min-mapq:5, mid-occ:5000
[M::main::202.242*1.07] stage2-specific parameters s2_bw:1000, s2_zdropinv:25
[M::mm_idx_stat] kmer size: 15; skip: 50; is_hpc: 0; #seq: 234214
[M::mm_idx_stat::202.337*1.07] distinct minimizers: 7146105 (31.16% are singletons); average occurrences: 22.090; average spacing: 25.344
[E::sam_parse1] **no SQ lines present in the header**
samtools view: error reading file "-"
[E::sam_parse1] no SQ lines present in the header
samtools view: error closing "-": -5

however，when I run with winnowmap -W repetitive_k9.txt -x map-pb --split-prefix -a -Y -L --eqx --MD --cs -t 60 ../hifi.fasta genome.fasta |samtools view -@ 20 -hb > read_alignment.bam [ERROR] --cs or --MD doesn't work with --split-prefix then I run whith out --cs or --MD winnowmap -W repetitive_k9.txt -x map-pb --split-prefix -a -Y -L --eqx -t 60 ../hifi.fasta genome.fasta |samtools view -@ 20 -hb > read_alignment.bam [main_samview] fail to read the header from "-".

marbl / Winnowmap

no SQ lines present in the header #39