Chromosome “whole genome shotgun sequence” not found

Chromosome “whole genome shotgun sequence” not found

2

Hello everyone, I hope that you´re okay

Today I’m trying to do an analysis with population 2 but before I have to bind my .bam files using mpileup. The problem is that when I try to bind the .bam files using mpileul the output shows a problem with the chromosomes.

This Is the problem: [E::faidx_fetch_seq] The sequence “NC_039898.1 Coffea arabica cultivar Caturra red isolate CCC135-36 chromosome 1c, Cara_1.0, whole genome shotgun sequence” not found

Someone can help me? I believe that is a problem with the genome reference but I’m not sure of that.

**The script that I’ m using is this:

samtools mpileup -B -f GCF_003713225.1_Cara_1.0_genomic.fna -Q20 -q20 MA_9BCOL_S8_L001_R1_001.paired_sorted.bam MA_9BCOL_S8_L001_R2_001.paired_sorted.bam>std.error.txt > pools_all3.mpileup


samtools


mpileup

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