Erick Cardenas

The script does not work anymore. Download from figshare was not possible either.

I have seen the same issue but in my case the step that kept the unpaired reads was Komplexity. You can check if that is the case by counting the...

I am getting the same error, grist cannot download a specific genome. In my case is GCF_006715245.1 When I checked the status of the genome in the (NCBI ftp)[https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/715/245/GCF_006715245.1_ASM671524v1/], the...

My solution: Change the snakefile from: Starting at line1062 ``` with open(output.genome, 'wb') as outfp: with urllib.request.urlopen(url) as response: content = response.read() outfp.write(content) print(f"...wrote {len(content)} bytes to {output.genome}", file=sys.stderr) ```...

I spent some time trying to get the data from other sources and I could not get it from the genbank or Gold but it is available from the JGI...

Yes, totally agree, the criteria for removal from the NCBI can vary and there is no way to know programatically.

I upgraded grist to 0.9.2 and run it again but snakemake if failing because it expects to have the genome downloaded as required in the rule output. I used the...

Yes on the config file. but I think I needed to clean files before rerunning. Originally I run genome-grist , and once it failed because of the missing error, I...

I removed the genbank_cache folder, the gather one, and the sig one too. Not sure if all of them were required.

I am getting an error at the make_gather_notebook_wc step. I run it with a simple sample. `Error in rule make_gather_notebook_wc: jobid: 1 input: /home/mixtures/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/../notebooks/report-gather.ipynb, grist/gather/Mock_T0_3_S3.gather.csv.gz, grist/gather/Mock_T0_3_S3.genomes.info.csv, grist/.kernel.set output: grist/reports/report-gather-Mock_T0_3_S3.ipynb, grist/reports/report-gather-Mock_T0_3_S3.html...