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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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samtools index: failed to create index for AK58.filter.Aligned.GeneTagged.sorted.bam": Numerical result out of range #254

Closed hcph closed 3 years ago

hcph commented 3 years ago

Describe the bug A clear and concise description of what the bug is. When I analysis the snRNA-seq data from wheat roots, the error comes [E::hts-idx-push] Region 536878855..536878953 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 'AK58.filtered.Aligned.GeneTagged.sorted.bam": Numerical result out of range. I add a '-c' in the line 145 of the zUMIs-dge2.R file: index_cmd<-paste(samtoolsexc, "index -c -@", opt$num_threads, outbamfile), However no work. So come here to ask you how to solve this problem. By the way, zUMIs is a amazing tools, I really love it.

cziegenhain commented 3 years ago

Hi,

Nice to hear that you like zUMIs! For this issue, it seems samtools indexing as we use it doesn't support chromosome longer than 512 Mb. We have only validated the tool with mammalian genomes. Are there any workarounds people with huge plant genomes typically do, like break up long genomes in several contigs in the reference?