Ragtag fails randomly

[johanneskoester]

Error in rule order_contigs:
    jobid: 75
    input: results/benchmarking/contigs/checked/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta, resources/genomes/main.fasta
    output: results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta
    log: logs/benchmarking/ragtag/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.log (check log file(s) for error details)
    conda-env: /github/workspace/.tests/.snakemake/conda/6ade157fc4182193208fad759df30bbf_
    shell:
        (ragtag.py scaffold -C -w -o results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold resources/genomes/main.fasta results/benchmarking/contigs/checked/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta && mv results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.fasta results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta) > logs/benchmarking/ragtag/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/benchmarking/ragtag/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.log:
================================================================================
Wed Nov  6 14:09:38 2024 --- VERSION: RagTag v2.1.0
Wed Nov  6 14:09:38 2024 --- CMD: ragtag.py scaffold -C -w -o results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold resources/genomes/main.fasta results/benchmarking/contigs/checked/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta
Wed Nov  6 14:09:38 2024 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.
Wed Nov  6 14:09:38 2024 --- INFO: Mapping the query genome to the reference genome
Wed Nov  6 14:09:38 2024 --- INFO: Running: minimap2 -x asm5 -t 1 /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/resources/genomes/main.fasta /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/checked/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta > /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.asm.paf 2> /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.asm.paf.log
Wed Nov  6 14:09:38 2024 --- INFO: Finished running : minimap2 -x asm5 -t 1 /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/resources/genomes/main.fasta /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/checked/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold.fasta > /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.asm.paf 2> /github/workspace/.tests/.snakemake/shadow/tmpb54bkjv2/results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.asm.paf.log
Wed Nov  6 14:09:38 2024 --- INFO: Reading whole genome alignments
Wed Nov  6 14:09:38 2024 --- INFO: Filtering and merging alignments
Traceback (most recent call last):
  File "/github/workspace/.tests/.snakemake/conda/6ade157fc4182193208fad759df30bbf_/bin/ragtag_scaffold.py", line 577, in <module>
    main()
  File "/github/workspace/.tests/.snakemake/conda/6ade157fc4182193208fad759df30bbf_/bin/ragtag_scaffold.py", line 488, in main
    raise RuntimeError("There are no useful alignments. Check output alignment files.")
RuntimeError: There are no useful alignments. Check output alignment files.
mv: cannot stat 'results/benchmarking/contigs/ordered-unfiltered/read-sample-B-1-351_READ_NUMBER_100_READ_LENGTH_100_STATE_scaffold/ragtag.scaffold.fasta': No such file or directory