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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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Effect of fungi and viruses #13

Closed wanxn518 closed 1 year ago

wanxn518 commented 1 year ago

Hello great developers, our macrogenome samples have sequences of higher abundance of fungi and viruses, when calculating the average genome size and average 16S copy number, do we need to remove these sequences first to avoid large errors？Hope to get your guidance.

pereiramemo commented 1 year ago

Hi!

We are happy to read that you find our tools useful. Yes, these tools were designed for prokaryotic metagenomes only. The addition of viruses and fungi sequences will add noise to the estimations. These should be removed as much as possible.

Cheers,

Emiliano

wanxn518 commented 1 year ago

Hello

Thank you very much for your reply, which is very helpful for our research.

Best, XiaoNan

pereiramemo commented 1 year ago

Hi,

I have a few questions:

  1. Is it always failing to run for the same samples?
  2. If it's consistently failing with the same samples, could you try to run these using fraggenescanplusplus within the run_ags.sh tool?
  3. Can you try to run it using --verbose?

Emiliano

On Wed, Mar 29, 2023 at 4:17 AM wanxn518 @.***> wrote:

Hello

Thank you very much for your reply, which is very helpful for our research. At the same time I have another problem, when I calculate the ags and acn, occasionally will show this error message：

~/apps/AGS-and-ACN-tools/run_ags.sh ../H3B11/H3B11.interleave.fa ../H3B11/H3B11.faa ../H3B11/H3B11-ags --sample_name H3B11 --overwrite t --save_complementary_data t #I provide the faa file predicted with FragGeneScanPlus uproc_prot failed

Some samples of tasks submitted at the same time will run normally with results, but some samples will have the error message that they cannot run. I don't know what the cause is, do you have any good suggestions ？

Best, XiaoNan

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