jeanzzhao

another genome missing: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/020/205/GCF_000020205.1_ASM2020v1/

> should I remove file like `GCF_000173095.1.info.csv` under `genbank_cache/` before starting the re-run?

@carden24 could you remind me which files you cleaned? thanks

- `pip install -U genome-grist`, v0.9.3., did not remove any previous file, sbatch #58672657, failed '/home/zyzhao/assloss/grist/marine44/.snakemake/log/2022-12-08T082206.462631.snakemake.log' ```== Building DAG of jobs... Updating job make_combined_info_csv_wc. Updating job copy_sample_genomes_to_output_wc. Updating job make_combined_info_csv_wc....

Hi Titus, - I realized that I did not have `rs207` in the folder when I changed `conf.yml` to `rs207`. - `curl -L https://osf.io/w4bcm/download -o gtdb-rs207.genomic-reps.k31.sbt.zip` - re-run, sbatch #58926209,...

sorry, some of my previous comments should be posted on a different issue (skip_genome), let me remove them.

dig into this one `SRR11593045` with @bluegenes , error in file below: `/home/zyzhao/assloss/grist/soil/.snakemake/log/2022-11-24T070134.689543.snakemake.log` ``` Job Missing files after 5 seconds: outputs.soil_samples/sigs/SRR11593045.trim.sig.zip This might be due to filesystem latency. If that...

> Re-run going for ~3h now, will update, thank you! @ctb

Re-run failed, different error (samtools_mpileup_wc) though: `farm:~/assloss/grist/marine21/.snakemake/log$ less 2022-12-08T155647.533690.snakemake.log` ``` Error in rule samtools_mpileup_wc: jobid: 22889 output: outputs.marine21_samples/leftover/SRR5915428.x.GCA_902550555.1.bcf, outputs.marine21_samples/leftover/SRR5915428.x.GCA_902550555.1.vcf.gz, outpu ts.marine21_samples/leftover/SRR5915428.x.GCA_902550555.1.vcf.gz.csi ... ```