Missing output file(s) `*assemblies_mqc.csv` expected by process `NFCORE_METATDENOVO:METATDENOVO:TRANSRATE

luciazifcakova commented 1 month ago

Description of the bug

What is "*assemblies_mqc.csv" and how can I create one? I have run my assembly on rnaspades (spades/3.15.5+dfsg-2) outside of the pipeline (with all samples together) and then I have copied the assembled files to pipeline results/spades folder and provided assembly to the pipeline. However, no file named "assemblies_mqc.csv" was created by spades... This files is not described in spades documentation, so where is it coming from?

Command used and terminal output

nextflow run nf-core/metatdenovo -r dev -resume '[intergalactic_mccarthy]' -profile oist --save_trimmed true --assembly /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta --skip_eggnog --eukulele_db gtdb --outdir /flash/MillerU/Vibrio_first_paper_data/results/ --input /flash/MillerU/Vibrio_first_paper_data/samples_for_first_vibrio_paper.csv

ERROR ~ Error executing process > 'NFCORE_METATDENOVO:METATDENOVO:TRANSRATE (/flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta)'

Caused by: Missing output file(s) *assemblies_mqc.csv expected by process NFCORE_METATDENOVO:METATDENOVO:TRANSRATE (/flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta)

Command executed:

transrate \ --threads 2 \ --assembly transcripts.fasta \ --output /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta_transrate \

mv /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta_transrate/assemblies.csv /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta_assemblies_mqc.csv

cat <<-END_VERSIONS > versions.yml "NFCORE_METATDENOVO:METATDENOVO:TRANSRATE": transrate: $(transrate --version) END_VERSIONS

Command exit status: 0

Command output: [ INFO] 2024-10-29 14:33:49 : Loading assembly: transcripts.fasta [ INFO] 2024-10-29 14:33:56 : Analysing assembly: transcripts.fasta [ INFO] 2024-10-29 14:33:56 : Results will be saved in /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta_transrate/transcripts [ INFO] 2024-10-29 14:33:56 : Calculating contig metrics... [ INFO] 2024-10-29 14:34:06 : Contig metrics: [ INFO] 2024-10-29 14:34:06 : ----------------------------------- [ INFO] 2024-10-29 14:34:06 : n seqs 235994 [ INFO] 2024-10-29 14:34:06 : smallest 73 [ INFO] 2024-10-29 14:34:06 : largest 10055 [ INFO] 2024-10-29 14:34:06 : n bases 96555122 [ INFO] 2024-10-29 14:34:06 : mean len 407.53 [ INFO] 2024-10-29 14:34:06 : n under 200 1939 [ INFO] 2024-10-29 14:34:06 : n over 1k 11489 [ INFO] 2024-10-29 14:34:06 : n over 10k 3 [ INFO] 2024-10-29 14:34:06 : n with orf 4775 [ INFO] 2024-10-29 14:34:06 : mean orf percent 51.89 [ INFO] 2024-10-29 14:34:06 : n90 246 [ INFO] 2024-10-29 14:34:06 : n70 298 [ INFO] 2024-10-29 14:34:06 : n50 388 [ INFO] 2024-10-29 14:34:06 : n30 706 [ INFO] 2024-10-29 14:34:06 : n10 1741 [ INFO] 2024-10-29 14:34:06 : gc 0.41 [ INFO] 2024-10-29 14:34:06 : bases n 454609 [ INFO] 2024-10-29 14:34:06 : proportion n 0.0 [ INFO] 2024-10-29 14:34:06 : Contig metrics done in 10 seconds [ INFO] 2024-10-29 14:34:06 : No reads provided, skipping read diagnostics [ INFO] 2024-10-29 14:34:06 : No reference provided, skipping comparative diagnostics [ INFO] 2024-10-29 14:34:06 : Writing contig metrics for each contig to /flash/MillerU/Vibrio_first_paper_data/results/spades/transcripts.fasta_transrate/transcripts/contigs.csv [ INFO] 2024-10-29 14:34:11 : Writing analysis results to assemblies.csv

Command error: [DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible. [DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.

Work dir: /flash/MillerU/Vibrio_first_paper_data/work/5e/77811d1cc91b56aa4f7f586fee340d

Container: /flash/MillerU/Vibrio_first_paper_data/work/singularity/depot.galaxyproject.org-singularity-transrate-1.0.3--hec16e2b_4.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

Relevant files

No response

System information

N E X T F L O W ~ version 24.10.0 HPC slurm Singularity CentOS Linux metatdenovo dev

erikrikarddaniel commented 1 month ago

The error comes from the TRANSRATE process that is calculating assembly statistics. We should try to fix this, so thanks for the report. I think you can safely ignore the error since the output from this process is not needed for anything downstream. To help the pipeline past this, you can add the below to a config file (easiest is editing or creating a nextflow.config in the work directory from where you run the pipeline, but also see: https://www.nextflow.io/docs/latest/config.html#configuration).

process {
    withName: TRANSRATE {
        errorStrategy = 'ignore'
    }
}

luciazifcakova commented 1 month ago

Thank you for prompt response. Ignoring the error with config file helped and now pipeline is running.

nf-core / metatdenovo