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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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Error in rule #707

Closed yustinus1 closed 6 months ago

yustinus1 commented 9 months ago

Hi Silas I'm Yustinus. I tried using atlas_metagenome but I got an error like the following:

Error in rule predict_genes: jobid: 681 input: Assembly/fasta/S028.fasta output: S028/annotation/predicted_genes/S028.fna, S028/annotation/predicted_genes/S028.faa, S028/annotation/predicted_genes/S028.gff log: S028/logs/gene_annotation/prodigal.txt (check log file(s) for error details) conda-env: /home/pipetin/databases/condaenvs/d4ac37792f743396b4b89995f71f7e75 shell:

    prodigal -i Assembly/fasta/S028.fasta -o S028/annotation/predicted_genes/S028.gff -d S028/annotation/predicted_genes/S028.fna             -a S028/annotation/predicted_genes/S028.faa -p meta -f gff 2> S028/logs/gene_annotation/prodigal.txt

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Logfile S028/logs/gene_annotation/prodigal.txt:

PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab Doug Hyatt, Loren Hauser, et al.

Request: Metagenomic, Phase: Training Initializing training files...done!

Request: Metagenomic, Phase: Gene Finding

Error: no input sequences to analyze.

===============================================

How to resolve the error. Thank You

SilasK commented 9 months ago

The error message states that there are no sequences in the assembly file. Check the input file. and then the assembly log.

yustinus1 commented 9 months ago

Thank you for your response.

I have checked the assembly file and the data is empty. Please help with the solution?

the script I use is: & atlas init --db-dir databases --working-dir WD1 /home/pipetin/Documents/Fastq_Metagenomics/optimization/ & atlas run qc --max-mem 0.95 (ATLAS finished) then continue & atlas run binning --max-mem 0.95 and error again. Assembly for fasta file is empty.

yustinus1 commented 9 months ago

when running I got a warning: [Sun Nov 12 20:24:38 2023] rule calculate_contigs_stats: input: Assembly/fasta/S035.fasta output: S035/assembly/contig_stats/final_contig_stats.txt log: S035/logs/assembly/post_process/contig_stats_final.log jobid: 639 reason: Missing output files: S035/assembly/contig_stats/final_contig_stats.txt; Input files updated by another job: Assembly/fasta/S035.fasta wildcards: sample=S035 resources: tmpdir=/tmp, mem=1, time=1, mem_mb=1000, mem_mib=954, time_min=60, runtime=60

Is this a problem?

SilasK commented 9 months ago

check the "{sample}/logs/assembly/spades.log"

And also the reports/QC_report.html

github-actions[bot] commented 7 months ago

There was no activity since some time. I hope your issue is solved in the mean time. This issue will automatically close soon if no further activity occurs.

Thank you for your contributions.