[E::hts_idx_push] chromosome blocks not continuous :Indexing of gff3 files using tabix error

Question

[chevivien]

Has anyone encountered this error before and could help? I am trying to index gff files using tabix in samtools and gt gff (genome tools) but getting errors.

I did this

grep -v "#"  sample.gff | sort -k1,1n -k4,4n -k5,5n | bgzip -c > sample2.gff3.gz 
tabix -p gff  sample2.gff3.gz

I get this error;

[E::hts_idx_push] chromosome blocks not continuous 
tbx_index_build failed: sample2.gff3.gz

I tried this again (Using genome tools)

grep -v "#"  sample.gff |gt gff3 -sort  > sample2.gff
bgzip -c sample2.gff
tabix -p gff  sample2.gff3.gz

I get this error

[E::hts_idx_push] chromosome blocks not continuous 
tbx_index_build failed: sample2.gff3.gz

I am using this sample gff file: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/704/415/GCF_001704415.1_ARS1/GCF_001704415.1_ARS1_genomic.gff.gz

Thanks

Answer 1

[cmdcolin]

I believe it would just be "sort -k1,1 -k4,4n" and not "sort -k1,1n -k4,4n" and the -k5,5n shouldn't be required. also when using genometools you need to use -sortlines, not just -sort

Depending on your usage of the tabix gff3, you might also consider this method http://biorxiv.org/content/early/2017/06/04/145938 which is important for jbrowse

[chevivien]

Thanks, this option sort -k1,1 doesn't work , sortlines in genome tools worked.