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Sorting of a bam file takes toooo long time

I am trying to use samtools sort function to sort a bam file (named as PT2) (size 180 megabite), which is not large. The sorting never end and no error message appeared. I have checked the memory of the VM Ubunto using (meminfo file in the proc folder on the home account). Also I have around 80 gig disc space

First code (extremely slow) :

samtools sort -o outputs/PT2_sorted.bam outputs/PT2.bam

second code (very slow):

samtools sort -o outputs/PT2_sorted.bam outputs/PT2.bam

What do you think is a reason behind this slow working ? any advice ?

Thanks

linux bam
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updated by Ram Ram • written by Mohamed Samir • Mohamed Samir

try to set the following options:

  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks can you provide a full code line ?

Thanks

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written by Mohamed Samir • Mohamed Samir

from the above suggestion

u can change -m value.

samtools sort -m 1G -T temp -o outputs/PT2_sorted.bam outputs/PT2.bam
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written by pbpanigrahi pbpanigrahi

That should be finished in like no time. Is the process even running? Use top to check. Please add comments via ADD REPLY.

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written by ATpoint ATpoint

Please use google and search for "linux top command". It shows you memory/CPU footprint of each running process, like Task Manager (Windows)/ Activity Monitor (macOS).

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written by Ram Ram

top to check, sorry was a typo, just open a terminal and type top, this shows an overview of active processes, and you should see samtools somewhere on top if it is running.

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written by ATpoint ATpoint

1 answer

That was resolved. The point was to increase the VM memory from 1024 to around 1800. This enabled running the command (even without adding -m or -T)

Thanks

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updated by Ram Ram • written by Mohamed Samir • Mohamed Samir

On a side note, your profile has a weird Google Scholar link. I guess it's because you posted your Scholar URL where only your ID was required. You should fix that as your profile does not point to your scholar profile at the moment.

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written by Ram Ram

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