Apple silicon M2

[mabouelk]

Have you tested Bactopia on M2? If so any tricks?

[rpetit3]

Hi @mabouelk

Thank you for reaching out!

Unfortunately at the moment no bioconda packages are available with arm64 builds. There is a way to emulate amd64 using Docker. It is a bit slower than native, but it at least is a bandaid until arm64 builds are available from Bioconda.

If you have docker installed and running, you can give it a try using -profile arm

Here's the test:

bactopia -profile test,arm

Again this is just a temporary solution, and hopefully native arm builds will come soon to Bioconda

Let me know how this goes for you!
Robert

[mabouelk]

thank you for your quick response. I've tried it on a mcabook pro with an interl processor but I got this
% bactopia --R1 sp12_S24_L001_R1_001.fastq.gz --R2 sp12_S24_L001_R2_001.fastq.gz --sample 12 --datasets datasets/ --outdir 12

2023-09-16 12:32:56 INFO 2023-09-16 12:32:56:root:INFO - download.py:544

                         Checking if environment pre-builds                 

                         are needed (this may take a while                  

                         if building for the first time)                    

                INFO     2023-09-16 12:32:56:root:INFO -     download.py:261

                         Begin gather create to                             

                         /Users/olaelsakhawy/.bactopia/conda                

                         /bioconda--bactopia-gather-1.0.4                   

2023-09-16 12:33:31 ERROR 2023-09-16 12:33:31:root:ERROR - download.py:374

                         Error creating Conda environment,                  

                         retrying after short sleep.                        

2023-09-16 12:34:07 ERROR 2023-09-16 12:34:07:root:ERROR - download.py:374

                         Error creating Conda environment,                  

                         retrying after short sleep.                        

2023-09-16 12:35:12 ERROR 2023-09-16 12:35:12:root:ERROR - download.py:374

                         Error creating Conda environment,                  

                         retrying after short sleep.                        

2023-09-16 12:36:47 ERROR 2023-09-16 12:36:47:root:ERROR - download.py:374

                         Error creating Conda environment,                  

                         retrying after short sleep.                        

2023-09-16 12:38:52 ERROR 2023-09-16 12:38:52:root:ERROR - download.py:374

                         Error creating Conda environment,                  

                         retrying after short sleep.                        

2023-09-16 12:41:42 ERROR 2023-09-16 12:41:42:root:ERROR - utils.py:43

                         External command failed with exit code             

                         1!                                                 

                                                                            

                         Command:                                           

                         bash -c 'mamba create -y -p                        

                         /Users/olaelsakhawy/.bactopia/conda/bio            

                         conda--bactopia-gather-1.0.4 -c                    

                         conda-forge -c bioconda --force                    

                         bioconda::bactopia-gather=1.0.4'                   

                                                                            

                         Standard output:                                   

                         conda-forge/osx-64                                 

                         Using cache                                        

                         conda-forge/noarch                                 

                         Using cache                                        

                         bioconda/osx-64                                    

                         Using cache                                        

                         bioconda/noarch                                    

                         Using cache                                        

                         r/osx-64                                           

                         Using cache                                        

                         r/noarch                                           

                         Using cache                                        

                         bioconda/osx-64                                    

                         Using cache                                        

                         bioconda/noarch                                    

                         Using cache                                        

                                                                            

                         Looking for:                                       

                         ['bioconda::bactopia-gather=1.0.4']                

                                                                            

                         Could not solve for environment specs              

                         The following package could not be                 

                         installed                                          

                         └─ bactopia-gather 1.0.4*  is not                  

                         installable because it requires                    

                            └─ sra-tools >=3.0.1 , which does               

                         not exist (perhaps a missing channel).             

N E X T F L O W ~ version 23.04.3

Launching /Users/olaelsakhawy/micromamba/envs/bactopia/share/bactopia-3.0.0/main.nf [zen_goldberg] DSL2 - revision: 0cd9f79ba7

WARN: Maximum memory (32) was adjusted to fit your system (16)

ERROR ~ ERROR: Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details

ERROR ~ * --outdir: expected type: String, found: Integer (12)

-- Check '.nextflow.log' file for details

WARN: Found unexpected parameters:

• --R2: sp12_S24_L001_R2_001.fastq.gz

• --R1: sp12_S24_L001_R1_001.fastq.gz

• Ignore this warning: params.schema_ignore_params = "R2,R1"

[rpetit3]

Unfortunately, another Mac related issue with Bioconda. There is not a build for sra-tools on Mac for recent versions. Going to to have to recommend Docker for you.

Also the parameters have changed in v3, R1 is now r1 similar for r2. Datasets are no longer needed as well

[mabouelk]

I don't have access to docker so I tried installing it on Linux and it worked just fine.
I am also wondering how can I run it on many files (~400 genomes of the same species) --BATCH RUN.
finally, I got an error for Graphvis "WARN: Graphviz is required to render the execution DAG in the given format" what is the best to install in path for the bactopia
Thank you again

[rpetit3]

Great!

To process multiple samples you will want to use bactopia prepare to create a sample sheet. Here are more details: https://bactopia.github.io/v3.0.0/beginners-guide/#multiple-samples