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Samtool sort Error

I did alignment with Hisat2 Human RNA-Seq sample from Illumina average sam file ~15.00GB in size I converted to bam file by using code

samtools view -S -b input. sam > output.bam

This created bam files with average size ~4.00GB size I checked the bam files for headers are othe stat which is looking good and don't think files are corrapted

now when I am trying to sort them with

samtools sort input.bam -o output.bam

it worked for a while and generated temporary bam files then start spitting on terminal with binary codes. and further no work even if I leave it to finishe. I also tried this code as felt may be this is due to memory problem

samtools sort @ 5 -m10G input.bam -o output.bam

Didn't work. I tried with other similar parameter to make it work but non working for me.

I am using CentOS7 with ~100GB ram and ~12TB on HDD

what I am doing wrong? please help.

rna-seq software error
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updated by ATpoint ATpoint • written by chimerajit • chimerajit

What is the samtools version? Maybe it is super old when -o was not introduced yet, therefore it is now spilling output to stdout(=screen).

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written by ATpoint ATpoint

Version 0.1.19-44428cd Not that I used same before and samtools sort [option] is showing -o.

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written by chimerajit • chimerajit

1 answer

That is the help from v0.1.19 which is ancient (from 2013), apparently -o was used back in the day to redirect to stdout. I suggest you update to the current one, then -o will capture the output to a file. If you want to use this one then do not use -o but do like samtool sort unsorted.bam sorted. Lots of improvements made until 2013 though, I'd upgrade.

./samtools sort

Usage:   samtools sort [options] <in.bam> <out.prefix>

Options: -n        sort by read name
         -f        use <out.prefix> as full file name instead of prefix
         -o        final output to stdout
         -l INT    compression level, from 0 to 9 [-1]
         -@ INT    number of sorting and compression threads [1]
         -m INT    max memory per thread; suffix K/M/G recognized [768M]
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written by ATpoint ATpoint

Thnaks, I'm updating hope this will work for me.

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written by chimerajit • chimerajit

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