Error while running test file

[SelfShubham]

While running following command nextflow run main_AMR++.nf -profile conda

N E X T F L O W ~ version 24.04.3

Launching main_AMR++.nf [elegant_gauss] DSL2 - revision: f6bfe39b99

A M R + + N F P I P E L I N E

reads being analyzed : /home/ncim/AMRplusplus-3.0.6/data/raw/*_R{1,2}.fastq.gz output folder : test_results

AMR++ Nextflow Pipeline Help
=============================

Available pipelines:
    - demo: Run a demonstration of AMR++
    - standard_AMR: Run the standard AMR++ pipeline
    - fast_AMR: Run the fast AMR++ pipeline without host removal.
    - standard_AMR_wKraken: Run the standard AMR++ pipeline with Kraken
Available pipeline subworkflows:
    - eval_qc: Run FastQC analysis
    - trim_qc: Run trimming and quality control
    - rm_host: Remove host reads
    - resistome: Perform resistome analysis
    - align: Perform alignment to MEGARes database
    - kraken: Perform Kraken analysis
    - qiime2: Perform QIIME 2 analysis
    - bam_resistome: Perform resistome analysis on BAM files

To run a specific pipeline/subworkflow, use the "--pipeline" option followed by the pipeline name:
    nextflow run main_AMR++.nf --pipeline <pipeline_name> [other_options]

To analyze your samples or otherwise change how AMR++ runs, modify the "params.config" file 
or add more parameters to the command line.

Finally, consider your computing environment and modify the "-profile" option. By default,
AMR++ assumes all software dependencies are in your $PATH, as in the "local" profile. Here are 
the other options:
    - local: Assumes all sofware is already in your $PATH
    - local_slurm: Local installation and adds control over slurm job submission.
    - conda: Uses "mamba" to install a conda environment. 
    - conda_slurm: Uses "mamba" and adds control over slurm job submission.
    - singularity: Uses a "singularity" image container.
    - singularity_slurm: Singularity image and adds control over slurm job submission.
    - docker: Uses a docker image container.

To include SNP analysis, add `--snp Y` to your command.

To include deduplicated count analysis, add `--deduped Y` to your command. 
Please be aware that adding deduplicated counts will significantly increase run time and temp file storage requirements.

=================================== Running a demonstration of AMR++

[- ] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Creating env using mamba: /home/ncim/AMRplusplus-3.0.6/envs/AMR++_env.yaml [cache /home/ncim/AMRplusplus-3.0.6/envs/AMR++_env-f6a872478a3709bc95dfc426aba819e3]

ERROR ~ Error executing process > 'FAST_AMRplusplus:FASTQ_QC_WF:fastqc (3)'

Caused by: Failed to create Conda environment command: mamba env create --prefix /home/ncim/AMRplusplus-3.0.6/envs/AMR++_env-f6a872478a3709bc95dfc426aba819e3 --file /home/ncim/AMRplusplus-3.0.6/envs/AMR++_env.yaml status : 1 message: Traceback (most recent call last): File "/home/ncim/anaconda3/bin/mamba", line 7, in from mamba.mamba import main File "/home/ncim/anaconda3/lib/python3.6/site-packages/mamba/mamba.py", line 53, in import mamba.mamba_api as api ImportError: /home/ncim/anaconda3/lib/python3.6/site-packages/mamba/mamba_api.cpython-36m-x86_64-linux-gnu.so: undefined symbol: archive_write_add_filter_zstd -- Check '.nextflow.log' file for details

Please help me to solve this error.

[susheelbhanu]

Your conda environment is missing 'mamba'. After you activate the AMR++_env, run the following: conda install conda-forge::mamba.

I had the same issue and this solved it.