dentist
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a-ludi
Close assembly gaps using long-reads at high accuracy.
Hi, I managed to run the pipeline but know I am having a closer look at the options. My goal is to be conservative with this: I ma happy to...
Hi, I've been trying to use dentist on the provided example dataset but a number of the md5 check sums after it finishes running are failing with no other errors...
When setting the parameters below, do these need to be included in the dentist.json config file? and if so in which section? --max-insertion-error --min-anchor-length --min-reads-per-pile-up --min-spanning-reads --allow-single-reads --join-policy
when I run "snakemake --configfile=snakemake.yml --use-conda" or "snakemake --configfile=snakemake.yml --use-conda --profile=slurm" it told me that "SyntaxError in line 920 of /public/home/GL_lixn/biosoft/dentist.v3.0.0.x86_64/Snakefile: Unexpected keyword container in rule definition (Snakefile, line 920)"
Hi again! I have now run dentist successfully a few times and tested the different join policies, using as input the raw contig assembly or a scaffold assembly, scaffolded with...
Hi, I am using ONT data and I got the error in the title from the pileupCollector (in the collect.log). I tried to increase the number of tolerated opened files...
I'm trying to use dentist on a docker container, but the example always fails during the `mask_self` step. From my mac, I'm starting the container using `docker run -it --rm=true...
Hi, I am using HiFi data to fill the gaps in a scaffold assembly. I get this error. I changed the latency to 15s from 5s I am running it...
``` (base) ubuntu@bio-xanthomonas:~/dentist-example$ snakemake --configfile=snakemake.yml --use-singularity --cores=all Pre-fetching singularity image... TypeError in line 45 of /home/djs217/dentist-example/Snakefile: __init__() got an unexpected keyword argument 'is_containerized' File "/home/djs217/dentist-example/Snakefile", line 745, in File "/home/djs217/dentist-example/Snakefile",...
