Param error on latest version of Grandeur #227
Comments
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That's... so strange. There must be a config file or something that has maxcpus set. I can't find anything in the directory. Is there something in your path by chance? Also, it looks like you are using version 3.0.20230205 as opposed to the most recent version. Do you know how that could be? |
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Did I improperly pull the latest version of Grandeur with the following? /data/Sequence_analysis/nextflow pull UPHL-BioNGS/Grandeur |
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I received this message after the pull: |
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Grandeur is on my machine here: |
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I found it in nextflow.config. |
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The current version should be 4.5.24250. I wonder why nextflow isn't pulling the latest one. Perhaps you can delete ~/.nextflow/assets/UPHL-BioNGS/Grandeur and re-pull the workflow? |
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Trying that.
Thanks!
Stephen M. Beckstrom-Sternberg, PhD
Bioinformatics Contractor
Arizona State Public Health Lab
Arizona Department of Health Services
Email: ***@***.***
… On Sep 10, 2024, at 3:59 PM, Young ***@***.***> wrote:
The current version should be 4.5.24250. I wonder why nextflow isn't pulling the latest one.
Perhaps you can delete ~/.nextflow/assets/UPHL-BioNGS/Grandeur and re-pull the workflow?
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I ran the latest version (Version: 4.5.24250), and now I am getting a singularity error: Caused by: |
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I was able to get a little further in the Grandeur analysis before failure, but it ran into the following 2 errors for Version: 4.5.24250:
-- Check script '/home/becksts/.nextflow/assets/UPHL-BioNGS/Grandeur/./subworkflows/../modules/local/prokka.nf' at line: 7 or |
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You encountered these errors at the same time? |
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Yes. |
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I found genome_sizes.json in UPHL-BioNGS/Grandeur/assets/genome_sizes.json |
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Yesterday's errors with singularity were due to nextflow_cachedir being empty on our new server, which I solved by copying the contents of nextflow_cachedir over from our old server. |
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Is there a way you can share the full error message with me? |
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Sure. I have attached nohup.out. Let me know if you need anything else. |
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It looks like it didn't even run! WTH is this? I wonder if it has anything to do with the |
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I reran without the iqtree2_outgroup param, and got this error: |
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It looks like there's something wrong with your Grandeur Ref container. What happens if you delete your quay.io-uphl-grandeur_ref-2024-06-26.simg file and redownload it? |
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OK. It was from the older server. Did you mean .img? And do I use nextflow pull? |
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Error with nextflow pull; |
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!!! It's missing !!! |
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Was this the correct command? |
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It would be something like |
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I found the "image" here: But the size is 0 for the "latest" and "2024-06-26" tags. |
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I chose to pull the latest image: It finished. It didn't place the image in /data/nextflow_cachedir. How do I find/test it? |
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That's a docker image. Did you want to convert it to a singularity image or just use Docker for the workflow? |
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I would prefer converting to a singularity image. What would the switch to docker entail? I get the same error when I call "-profile docker,msa": N E X T F L O W ~ version 24.04.4 Launching /^^^^ /^^^^^^^ /^ /^^^ /^^ /^^^^^ /^^^^^^^^ /^^ /^^ /^^^^^^^ Author: Erin Young -- Check script '/home/becksts/.nextflow/assets/UPHL-BioNGS/Grandeur/./subworkflows/../modules/local/prokka.nf' at line: 7 or see '.nextflow.log' file for more details |
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My apologies for taking so long to get back to you!!! It might be your version of singularity, but this is one issue that I've seen before. Nextflow will pull your singularity images and store them in your singularity cache directory. If not, this is how you create a singularity image using both docker and singularity. This specific image will need to be named "quay.io-uphl-grandeur_ref-2024-06-26.img" and put in your nextflow singularity cachedir, which I think is |
I am running the latest version of Grandeur and erroneously getting an error (maxcpus isn't a supported param), even though I am not using that param. Here is my command-line and the error message: ./nextflow run -qs 10 UPHL-BioNGS/Grandeur -profile singularity,msa --iqtree2_outgroup NZ_CP043953.1 --outdir grandeur
N E X T F L O W ~ version 24.04.4
Launching
https://github.com/UPHL-BioNGS/Grandeur[lethal_cajal] DSL2 - revision: 35b867a [main]/^^^^ /^^^^^^^ /^ /^^^ /^^ /^^^^^ /^^^^^^^^ /^^ /^^ /^^^^^^^
/^ /^^ /^^ /^^ /^ ^^ /^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^
/^^ /^^ /^^ /^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^
/^^ /^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^^^^^ /^^ /^^ /^ /^^
/^^ /^^^^ /^^ /^^ /^^^^^^ /^^ /^^ /^ /^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^
/^^ /^ /^^ /^^ /^^ /^^ /^^ /^ ^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^
/^^^^^ /^^ /^^ /^^ /^^ /^^ /^^ /^^^^^ /^^^^^^^^ /^^^^^ /^^ /^^
Currently using the Grandeur workflow for use with microbial sequencing.
The view is great from 8299 feet (2530 meters) above sea level.
Author: Erin Young
email: [email protected]
Version: 3.0.20230205
FATAL: maxcpus isn't a supported param!
Supported params: [outdir, fastas, msa, kraken2_db, mash_db, config_file, reads, sample_sheet, fasta_list, blast_db, blast_db_type, fastani_ref, fastani_ref_list, iqtree2_outgroup, genome_sizes, sra_accessions, minimum_reads, datasets_max_genomes, mash_max_hits, min_core_genes, current_datasets, skip_extras, exclude_top_hit, aligner]
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