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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
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samtools view: failed to add PG line to the header #83

Closed Labarcena-Jessica closed 8 months ago

Labarcena-Jessica commented 8 months ago

Hello Marcela,

I was wondering if you have an idea how to solve this error. I am not sure what's happening. It comes after the pipeline runs this line [INFO] minimap2 -t 4 --secondary=no -ax map-pb all_potential_contigs.fa gbk.HiFiMapped.bam.fasta | samtools view -@ 4 -b -F4 -F 0x800 -q 0 -o HiFi-vs-potential_contigs.bam

[W::sam_hdr_create] Duplicated sequence "ptg000001c_rc_rotated" in file "-" [E::sam_hrecs_update_hashes] Duplicate entry "ptg000001c_rc_rotated" in sam header samtools view: failed to add PG line to the header

Thank you!

Jessica

Labarcena-Jessica commented 8 months ago

This error doesn't occur when running the pipeline with the contigs, so if anyone is having this issue, just run the pipeline with the contigs after running Hifiasm.