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there is an error after samtools index

Hi, there is an error occuring after the following command

[E::hts_idx_push] Unsorted positions on sequence #4: 27130750 followed by 27130362

samtools index: failed to create index for "1_sorted.bam"

and my samtools sort command is

samtools sort 1_raw.bam -n -m 2G -@ 4 -o 1_sorted.bam

[bam_sort_core] merging from 8 files and 4 in-memory blocks...

I want to know where is the problem,who can give we some advice on the error??

dna-seq
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updated by swbarnes2 swbarnes2 • written by 543541656 • 543541656

(remove the -n option); It is because the -n option is sorted by name.

 -n         Sort by read name

Index, requires the bam file sorted by Coordinates.

See the manual of samtools: http://www.htslib.org/doc/samtools-index.html

Index a coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast random access.

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written by wm wm

thank you,I have solved the problem according to your requirements

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written by 543541656 • 543541656

1 answer

Is there a reason you are sitting by name? It looks like you can't index a bam so sorted.

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written by swbarnes2 swbarnes2

no,I just copy someone else's code,because it is the first time to use that for me.

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written by 543541656 • 543541656

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