[2024-12-04T23:43:21Z INFO  lrge] Running two-set strategy with 10000 target reads and 5000 query reads
Error: Failed to generate estimate

Caused by:
    Too few reads requested: Number of reads in FASTQ file (1) is <= query number of reads (5000)
[Thu Dec  5 07:43:21 2024]
Error in rule lrge:
    jobid: 4
    input: 02_fastq/BA00000001.fastq.gz
    output: 03_assembly/03.1_hybracter/BA00000001/processing/chrom_size/BA00000001_lrge_estimated_chromosome_size.txt
    log: 03_assembly/03.1_hybracter/BA00000001/stderr/lrge/BA00000001.log (check log file(s) for error details)
    conda-env: /home/gilmansiu3/miniforge3/envs/hybracter-v0.11.0/lib/python3.12/site-packages/hybracter/workflow/conda/024e350392d5612938570ada6f9b3299_
    shell:
        
        if [[ 02_fastq/BA00000001.fastq.gz =~ \.gz$ ]]; then
        INPUT_CMD="zcat 02_fastq/BA00000001.fastq.gz"
        else
        INPUT_CMD="cat 02_fastq/BA00000001.fastq.gz"
        fi

        # Now run the awk command on the decompressed file
        if $INPUT_CMD | awk '{if (NR % 4 == 1) count++} END {exit count > 10000 ? 0 : 1}'; then
            # There are more than 10,000 reads, run lrge with defaults
            lrge -t 8 -s 42 02_fastq/BA00000001.fastq.gz -o 03_assembly/03.1_hybracter/BA00000001/processing/chrom_size/BA00000001_lrge_estimated_chromosome_size.txt
        else
            # There are less than 10,000 reads, use the all-vs-all strategy with all available reads
            lrge -t 8 -s 42 -n 10000 02_fastq/BA00000001.fastq.gz -o 03_assembly/03.1_hybracter/BA00000001/processing/chrom_size/BA00000001_lrge_estimated_chromosome_size.txt
        fi

        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile 03_assembly/03.1_hybracter/BA00000001/stderr/lrge/BA00000001.log not found.

Removing output files of failed job lrge since they might be corrupted:
03_assembly/03.1_hybracter/BA00000001/processing/chrom_size/BA00000001_lrge_estimated_chromosome_size.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-12-05T074308.272662.snakemake.log
WorkflowError:
At least one job did not complete successfully.
[2024:12:05 07:43:21] ERROR: Snakemake failed