Issue running Natrix2 with Nanopore 18S example data

dbeisser / Natrix2

Open-source bioinformatics pipeline for the preprocessing of raw amplicon sequencing / metabarcoding data.

MIT License

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Issue running Natrix2 with Nanopore 18S example data #11

Closed MP-98-21 closed 5 months ago

MP-98-21 commented 7 months ago

Hello,

I was trying to run Natrix2 on the example data provided. It works correctly with the Illumina data but when trying to use the Nanopore data it gives the following error: Pychopper_error

I also attached a screenshot of the files contained in the Natrix2 folder. It seems the error is related to pychopper but I was able to install it correctly in the conda environment. I also tried using the dev version of Natrix2 and had the same error.

Natrix2_files

Any help or guidance you may have is appreaciated.

Thank you very much, Miguel

DanaBlu commented 7 months ago

Hi Miguel,

thank your for reporting this issue!

Please make sure that your dev-branch is up to date. "KeyError" usually refers to discrepancies between the file names of the csv file and the file names of the data folder. Please also check if the correct name of the data folder is specified in the yaml configuration file.

For nanopore sequences, we currently recommend using the dev-branch until we merge it with the main branch.

Please feel free to contact us anytime if you are running into other issues!

Best,

Dana

MP-98-21 commented 5 months ago

Hi Dana,

Thank you for your help! Using the dev-branch and running the example Nanopore data worked, but we are having issues running Natrix with our own data. We are having an error in the rule "make_ncbi_db", where it says some files "nt.000." files were not downloaded correctly or maybe corrupt. And the pipeline won't work due to this.

We tried replacing these files with manually downloaded ones from NCBI but the error persists. And trying the options it gives us with the snakemake commands are not working as we get an error in the Snakefile:

I also attached the log file of the natrix run. 2024-06-11T122121.907859.snakemake.log We would appreaciate it if you could help us solve this.

Thank you for your help and your time!

Greetings, Miguel

dusti1n commented 5 months ago

Hi Dana,

Thank you for your help! Using the dev-branch and running the example Nanopore data worked, but we are having issues running Natrix with our own data. We are having an error in the rule "make_ncbi_db", where it says some files "nt.000." files were not downloaded correctly or maybe corrupt. And the pipeline won't work due to this.

We tried replacing these files with manually downloaded ones from NCBI but the error persists. And trying the options it gives us with the snakemake commands are not working as we get an error in the Snakefile:

I also attached the log file of the natrix run. 2024-06-11T122121.907859.snakemake.log We would appreaciate it if you could help us solve this.

Thank you for your help and your time!

Greetings, Miguel

The question has been transferred to the following contribution: https://github.com/dbeisser/Natrix2/issues/15