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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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Two errors with v3.0.3 #23

Closed Isabella136 closed 1 year ago

Isabella136 commented 1 year ago

So two errors appear when trying to run v3.0.3

The first is an issue with one of the process label specified in fastqc.nf:

ERROR ~ Not a valid process label: Run multiqc -- Label must consist of alphanumeric characters or '_', must start with an alphabetic character and must end with an alphanumeric character

 -- Check script 'subworkflows/../modules/Fastqc/fastqc.nf' at line: 28 or see '.nextflow.log' file for more details

The second one is an issue with the input reads:

Cannot find any reads matching: /blue/boucher/nbonin/AMRplusplusv303/AMRplusplus/data/raw/*_R{1,2}.fastq.gz

However, I just checked and all of the files are present in the data/raw/ directory:

ls data/raw/
S1_test_R1.fastq.gz  S1_test_R2.fastq.gz  S2_test_R1.fastq.gz  S2_test_R2.fastq.gz  S3_test_R1.fastq.gz  S3_test_R2.fastq.gz
felipemachado85 commented 1 year ago

Hi Isabela,

It seems you have a problem with your initial input for multiqc. I would suggest looking over your fastq files to see if they're ok (try running them in a standalone QC like Fastqc to check if they're ok).

For the second problem, I would recommend creating a new folder containing your sequences inside the AMRplusplus folder (this raw/data folder contains files pertaining to the demo pipeline), so your path would be significantly reduced. I had the same problem and when it worked when I did this.

I hope this could be of any help to you!

Isabella136 commented 1 year ago

I'm actually using the demo fastq files, so I doubt that the issue comes from there.

The first issue comes from the "Run multiqc" label in the fastqc.nf file; nextflow doesn't seem to accept a label with a space character.

I have yet to test v.3.0.4, but based on the code modifications, it should have fixed both errors.

EnriqueDoster commented 1 year ago

@Isabella136 and @feli ,

Yeah thanks for catching this, I was making little mistakes and incorrectly named a label for a process. Somehow this also causes the error to show that the test reads were not found. The latest code fixes this and it should work fine now. Thanks!