Bug Report: samtools index failed — "Region ... cannot be stored in a bai index"

[wangdachui221]

1. Description

When running CIRIquant for a large genome (Ginkgo), the pipeline fails at the samtools index step with the following error:

[E::hts_idx_push] Region 536887082..536887449 cannot be stored in a bai index.
Try using a csi index with min_shift = 14, n_lvls >= 6
samtools index: failed to create index for "xxx.sorted.bam": Numerical result out of range

This error did not occur in a previous successful run on another species (poplar, smaller genome).

2. System and Software Info
   CIRIquant-1.1.3
   conda activate ciriquant_py27
   conda install -c bioconda bwa=0.7.17 hisat2=2.1.0 stringtie=1.3.5 samtools=1.9

3. YAML Config

Ginkgo.yml

name: Ginkgo
tools:
bwa: /home/user/.conda/envs/ciriquant_py27/bin/bwa
hisat2: /home/user/.conda/envs/ciriquant_py27/bin/hisat2
stringtie: /home/user/.conda/envs/ciriquant_py27/bin/stringtie
samtools: /home/user/.conda/envs/ciriquant_py27/bin/samtools

reference:
fasta: /data/user/cirRNA/ginkgo/00data/Gbi_chr.fa
gtf: /data/user/cirRNA/ginkgo/00data/gbi.gtf
bwa_index: /data/user/cirRNA/ginkgo/00data/Gbi_chr.fa
hisat_index: /data/user/cirRNA/ginkgo/00data/Gbi_chr.fa

4. Run Script
   #!/bin/bash
   THREADS=60

for fq1 in *_noRibo.fq.1.gz; do
fq2=${fq1/.fq.1.gz/.fq.2.gz}
sample=${fq1%_noRibo.fq.1.gz}

echo "==== Processing sample: $sample ===="

CIRIquant -t $THREADS \
    -1 "$fq1" \
    -2 "$fq2" \
    --config /data/xlin/cirRNA/ginkgo/00data/Ginkgo.yml \
    -o "./CIRIquant_${sample}" \
    -p "$sample" \
    -l 2

echo "==== Finished sample: $sample ===="

done

May I ask if there is any recommended solution for this issue in the current version?