lra index stops without error

[imdanique]

Hi! I'm using this pipeline (https://github.com/nanoporetech/pipeline-structural-variation) which uses LRA, however it accidentally abrupts during lra index. So, I tried to use LRA index independently, and it still doesn't work. I've tried hg38 reference genome from different sources and still have the same issue.

sudo -E env "PATH=$PATH" lra index -ONT /data/ont/hg38/Homo_sapiens_assembly38.fasta
Sorting 648549399 minimizers
done Sorting
555566865 minimizers with multiplicity samller than 150
There are 181535077 minimizers left

LRA just stops without any error here. Do you have any idea what I'm doing wrong and how to solve this? Thanks!

[mchaisso]

Do you have at least 32G allocated to the job to generate the index? This much isn't necessary for hg38, but it will rule out memory issues.

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On Thu, Jun 3, 2021 at 11:45 PM Daniyar Karabayev ***@***.***> wrote: Hi! I'm using this pipeline ( https://github.com/nanoporetech/pipeline-structural-variation) which uses LRA, however it accidentally abrupts during lra index. So, I tried to use LRA index independently, and it still doesn't work. I've tried hg38 reference genome from different sources and still have the same issue. sudo -E env "PATH=$PATH" lra index -ONT /data/ont/hg38/Homo_sapiens_assembly38.fasta Sorting 648549399 minimizersdone Sorting 555566865 minimizers with multiplicity samller than 150 There are 181535077 minimizers left LRA just stops without any error here. Do you have any idea what I'm doing wrong and how to solve this? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#19>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKPGPSXKSIUVJNYWUUBYNTTRBZB7ANCNFSM46CF76LQ> .

[imdanique]

@mchaisso, Thank you for your quick response! Yes, I have more than 300 GB of available ram and more than 700 GB of free space

[mchaisso]

Can you make sure you have lra>=1.3.0 ?

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On Fri, Jun 4, 2021 at 10:00 AM Daniyar Karabayev ***@***.***> wrote: @mchaisso, Thank you for your quick response! Yes, I have more than 300 GB of available ram and more than 700 GB of free space — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[imdanique]

@mchaisso , I had 1.2 and updated it to 1.3.0, still have the same issue

[imdanique]

I've tried to use an alternative with minimap2, but has the same issue, which is strange

[syngnathid]

I have the same issue and the server has ~1TB RAM. Is there a way to specify the allocated memory to lra?

I used the following command.

# Installed on 2022-Feb-16
# lra v1.3.2 via bioconda
mamba install -c bioconda lra
lra index -CCS ref.fa 

Here is the output after a few seconds.

Sorting 89435573 minimizers
done Sorting
70589499 minimizers with multiplicity smaller than 150
There are 22508006 minimizers left

I tried minimap2 and I have no issues!

[ziphra]

Hello, I thought I had the same issue.
But it appeared that in my case the indexing is fine and completed, it's just that the output files are stored in the same directory as the reference file provided, not my current working directory.