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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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Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_R1) #13

Closed priscillaisaac98 closed 1 year ago

priscillaisaac98 commented 1 year ago

Run this command: nextflow run main_AMR++.nf --help

But it shows this error; Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test)'

Caused by: No such variable: TRIMMOMATIC -- Check script 'subworkflows/../modules/Trimming/trimmomatic.nf' at line: 43

Source block: """ ${TRIMMOMATIC} \ PE \ -threads ${threads} \ ${reads[0]} ${reads[1]} ${sample_id}.1P.fastq.gz ${sample_id}.1U.fastq.gz ${sample_id}.2P.fastq.gz ${sample_id}.2U.fastq.gz \ ILLUMINACLIP:${adapters}:2:30:10:3:TRUE \ LEADING:${leading} \ TRAILING:${trailing} \ SLIDINGWINDOW:${slidingwindow} \ MINLEN:${minlen} \ 2> ${sample_id}.trimmomatic.stats.log

  """

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

Anyone can help me out with this?

EnriqueDoster commented 1 year ago

Hi @priscillaisaac98, thank you for reporting this. We found that we would sometimes have issues with the parsing of environmental variables and have now updated how this is handled. Please try the updated AMR++ (v3.0.1) code and let us know if you run into any issues. Thank you!

priscillaisaac98 commented 1 year ago

Hi,

I tried the latest AMR++(v3.0.1) code and still got an error but this time with a different error. It showed :Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (Virome1)'; Caused by: Process FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (Virome1) terminated with an error exit status (1). Is there any idea how I can solve this? Thank you.

Regards, Priscilla

[image: image.png] [image: image.png]

On Mon, 10 Apr 2023 at 07:35, EnriqueDoster @.***> wrote:

Hi @priscillaisaac98 https://github.com/priscillaisaac98, thank you for reporting this. We found that we would sometimes have issues with the parsing of environmental variables and have now updated how this is handled. Please try the updated AMR++ (v3.0.1) code and let us know if you run into any issues. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/Microbial-Ecology-Group/AMRplusplus/issues/13#issuecomment-1501237745, or unsubscribe https://github.com/notifications/unsubscribe-auth/A44IA44MWGHHQ2M2NMENR2TXANBSTANCNFSM6AAAAAAVTI3FKY . You are receiving this because you were mentioned.Message ID: @.***>