binchicken single --forward bc/test/data/sample_1.1.fq bc/test/data/sample_2.1.fq bc/test/data/sample_3.1.fq --reverse bc/test/data/sample_1.2.fq bc/test/data/sample_2.2.fq bc/test/data/sample_3.2.fq --output binchicken_single_assembly --run-aviary --assembly-strategy megahit --aviary-gtdbtk-db /work/river/Databases/GTDBTk/release226/ --aviary-checkm2-db /work/river/Databases/checkm2/CheckM2_database/ --aviary-skip-binners semibin --cores 1 &>log
(binchicken) (conda)aquarius01:20251118:~/git/binchicken$ grep -c '^localrule aviary_recover' log
12
That fails because of a divide by zero error in CoverM (I think) caused by a tiny test dataset. A spearate problem.
The issue here is that the binchicken attempts 4 times, but in each of those, aviary retries 3 times, so it adds up to a lot. Maybe binchicken should set aviary retries to 1, or just let aviary do the retrying by itself so as not to duplicate work (I'm thinking option 2 might be better).
That fails because of a divide by zero error in CoverM (I think) caused by a tiny test dataset. A spearate problem.
The issue here is that the binchicken attempts 4 times, but in each of those, aviary retries 3 times, so it adds up to a lot. Maybe binchicken should set aviary retries to 1, or just let aviary do the retrying by itself so as not to duplicate work (I'm thinking option 2 might be better).