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Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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SNP broken in AMRplusplus #21

Closed CarstenBaker closed 1 year ago

CarstenBaker commented 1 year ago

Using the latest version of AMRplusplus (v3.0.2) and running this command for testing I get the following SNP errors:

nextflow run main_AMR++.nf -profile singularity --snp Y

Error

[aa/b2d3c7] NOTE: Process `FAST_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (S3_test)` terminated with an error exit status (1) -- Error is ignored
[9c/de97f2] NOTE: Process `FAST_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (S1_test)` terminated with an error exit status (1) -- Error is ignored
[da/82c3d1] NOTE: Process `FAST_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (S2_test)` terminated with an error exit status (1) -- Error is ignored

Looking at the .command.err file I get

  File "SNP_Verification.py", line 275
    with (open(config['FULL_FILE_NAMES']['NTYPE_OUTPUT'], "w") as outputN,
                                                                ^
SyntaxError: invalid syntax

AmrPlusPlus_SNP has been updated to use >Python 3.9 but the singularity container for Amrplusplus still uses python 3.7.4 so will no longer work unless I am missing something obvious ?

Can you let me know if I am missing some guide for getting SNP working with AMRplusplus using singularity ?

Isabella136 commented 1 year ago

@EnriqueDoster is it possible to update the singularity container so that it works with python 3.9, or do I need to make a version of AmrPlusPlus_SNP that is compatible with the current container?

EnriqueDoster commented 1 year ago

@CarstenBaker and @Isabella136 ,

Let me work on updating the singularity container ASAP! Sorry for the delay and thanks for bringing this to my attention!

In the meantime, you can also try the local conda installation. I'll close this issue for now but count on the singularity container being updated by the end of the day. Thanks!