(Kallisto) samtools index error: Region 4115678..540982422 cannot be stored in a bai index

Question

[liying]

Hi, everyone! I used kallisto --genomebam to generate genomic bam files, but the bam files can't be indexed, and kallisto (using samtools index) raised the error: [E::hts_idx_push] Region 4115678..540982422 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6

[log file]:

[quant] fragment length distribution is truncated gaussian with mean = 200, sd = 20
[index] k-mer length: 31
[index] number of targets: 316,278
[index] number of k-mers: 240,920,543

[index] number of equivalence classes: 1,287,153
[quant] running in single-end mode
[quant] will process file 1: /data/projects/lncRNA/Gene-Expression/mm10/Raw-Data/ENCFF910RNP-ENCFF916XIQ-ENCFF919VVI.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 42,452,418 reads, 31,051,815 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,485 rounds
[  bam] writing pseudoalignments to BAM format .. done
[  bam] sorting BAM files .. done
[  bam] indexing BAM file .. [E::hts_idx_push] Region 4115678..540982422 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
 invalid return code when indexing file -1 .. done

And then, I checked the bam file, but the max position of this bam file is 195323384 from chr1, it’s not exceed the the range of chr1. I don't why samtools can't index that file....

Could someone give me some suggestions?

Answer 1

[liying]

OK！ I knew it! It resulted from my GTF file. reference: https://github.com/pachterlab/kallisto/issues/155 pmelsted and mfansler solved my problems.