NextPolish fails with Short and Long Reads

[steinbrl]

I use Nextpolish on an HPC cluster, which is working flawless, if I use only short reads. But after activating the hybrid option (sgs+lgs), then it fails, delivering the following error massage. It is obviously a problem of minimap2. I try to polish several contigs from the same genome, with different lengths in an multi fasta file. It is an viral genome, cloned in an BAC, with terminal repeats, which fit on each other, some contigs are shorter than the full genome, some have "over-assembly" and are longer. Could this be the problem?

hostname

• hostname cd /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/00.lgs_polish/02.map.ref.sh.work/map_genome2
• cd /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/00.lgs_polish/02.map.ref.sh.work/map_genome2 ( minimap2 --split-prefix tmp -a -x map-ont -t 5 /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/00.lgs_polish/input.genome.fasta /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/input.lgspart.001.fasta.gz|samtools view --threads 5 -F 0x4 -b - |samtools sort - -m 2g --threads 5 -o lgs.part001.sort.bam )
• minimap2 --split-prefix tmp -a -x map-ont -t 5 /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/00.lgs_polish/input.genome.fasta /hpc/project/vir-ngs/Rundir/Hybrid_Assembly_Herpesviridae/HSV1_KSHV_BACs_04_2024/next_hybrid/nextpolish/01_rundir/input.lgspart.001.fasta.gz
• samtools view --threads 5 -F 0x4 -b -
• samtools sort - -m 2g --threads 5 -o lgs.part001.sort.bam minimap2: unrecognized option: split-prefix [ERROR] failed to open file 'tmp' [main_samview] fail to read the header from "-". [W::hts_set_opt] Cannot change block size for this format samtools sort: failed to read header from "-"

[steinbrl]

Solved! After installing the newest Minimap2 version, it works flawless now... :) Conda installed an very outdated version of Minimap2.