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pereiramemo / AGS-and-ACN-tools

Fast and accurate Average Genome Size and 16S rRNA gene Average Copy Number computation in metagenomic data
GNU General Public License v3.0
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memory -m option of SortMeRNA error #8

Closed brittanysuttner closed 3 years ago

brittanysuttner commented 3 years ago

Hello, I am using acn.sh on MacOS with Docker and running with TARA test data and get the following error (I tried with and without explicitely stating the --smrna_mem option and still get the same error):

./run_acn.sh tara_ags_output/tara_023_srf_FBL.fna tara_ags_output/tara_023_srf_ags.tsv tara_acn_output --evalue 1e-10 --min_identity 80 --min_length 30 --verbose t --overwrite t --nslots 2 --save_complementary_data t --smrna_mem 1024 Unable to find image 'epereira/acn:latest' locally latest: Pulling from epereira/acn 423ae2b273f4: Pull complete de83a2304fa1: Pull complete f9a83bce3af0: Pull complete b6b53be908de: Pull complete c38428f8001a: Pull complete 74ca5d8a314e: Pull complete fd176dc9124e: Pull complete fe5a592d6031: Pull complete 48a1c334397a: Pull complete 2bde6447fd7a: Pull complete 229602989b4b: Pull complete 2791a3f3906d: Pull complete 01ca4b6b4e64: Pull complete 9e0af1d426c0: Pull complete 58ef52b995e9: Pull complete 0a8390a31b2c: Pull complete 56a089dbf60d: Pull complete a45353e2dc59: Pull complete 49db43483422: Pull complete 7fd0473b9cdf: Pull complete 12302c07b075: Pull complete 64a1159ae245: Pull complete 65185568e3bd: Pull complete c5f99cb58ace: Pull complete Digest: sha256:d8aeeeebbf83f3d25911edbf0554e41c0c5d4bc85342f86597f815eabdf0e0e1 Status: Downloaded newer image for epereira/acn:latest Identifying 16S rRNA genes ...

ERROR: -m [INT] must not exceed 1989 (Mbyte).

SortMeRNA failed

pereiramemo commented 3 years ago

Hi!

Thanks for using our tools. Could please tell me what MacOS are you using? A user had this issue once, but I haven't been able to reproduce it. It appears to be related to how Docker works in Mac.

I am sorry but I don't have a real solution, just two workarounds:

  1. If possible use a Linux computer (also, Docker works better in Linux).
  2. If you can install and run the SortMeRNA tool on your Mac computer, you could use the blast formatted tabular output of this tool to run the acn.sh tool (see https://github.com/pereiramemo/AGS-and-ACN-tools/wiki/Documentation#2-acnsh).

Let me know if this was clear enough or if you have other questions.

Best,

Emiliano

brittanysuttner commented 3 years ago

Hello, My version of MaOS is Sierra 10.12.6 Yes I have SortMeRNA output for my data and will try the workaround you suggested. Thanks.

On Thu, Dec 17, 2020 at 11:04 PM Emiliano Pereira Flores < notifications@github.com> wrote:

Hi!

Thanks for using our tools. Could please tell me what MacOS are you using? A user had this issue once, but I haven't been able to reproduce it. It appears to be related to how Docker works in Mac.

I am sorry but I don't have a real solution, just two workarounds:

  1. If possible use a Linux computer (also, Docker works better in Linux).
  2. If you can install and run the SortMeRNA tool on your Mac computer, you could use the blast formatted tabular output of this tool to run the acn.sh tool (see https://github.com/pereiramemo/AGS-and-ACN-tools/wiki/Documentation#2-acnsh ).

Let me know if this was clear enough or if you have other questions.

Best,

Emiliano

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pereiramemo commented 3 years ago

Good! Just make sure the sortmerna blast output is tabulated like this: http://www.metagenomics.wiki/tools/blast/blastn-output-format-6

Best,

Emiliano