User: benv

gravatar for benv
benv620
Reputation:
620
Status:
Trusted
Location:
Canada
Last seen:
2 days, 22 hours ago
Joined:
2 years, 11 months ago
Email:
b***@bcgsc.ca

Posts by benv

<prev • 74 results • page 1 of 8 • next >
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Comment: C: SNP calling from a scaffold.fa file
... Thanks, @pfs! I was just about to suggest the same. ...
written 9 days ago by benv620
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Comment: C: Reading single-end reads takes forever
... Sorry for slow response. To run a single-end assembly only, specify the input single-end reads with `se=""` or `in=""` and add the word "unitigs" to the end of the `abyss-pe` command. ...
written 10 weeks ago by benv620
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Comment: C: ABySS and Velvet "number of contigs and contig length in pair-end and single-en
... I am not familiar with Velvet usage, but if you provide the `abyss-pe` command and verbose log output (add "v=-v" to `abyss-pe` command), I could have a look. Output of `abyss-fac` (N50 etc.) is helpful as well. It is standard practice to run assemblies for a range of k-mer sizes to achieve the be ...
written 10 weeks ago by benv620
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Comment: C: Bosst configure error
... It is really hard to tell what is wrong from the `configure` output alone. If you look for the Boost checks in the `config.log` file it will give you more info about why the checks failed. If you like, you can post your config.log (post here, send e-mail to benv at bcgsc dot ca, or post to GitHub ...
written 12 weeks ago by benv620
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Comment: C: Rescaffolding a genome assembly?
... Good to know. Thanks for posting back! ...
written 3 months ago by benv620
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Comment: C: What happened after coverage.hist in Abyss?
... 500 GB might not be enough unfortunately. Your `abyss-pe` command looks good. The ABySS log contains messages indicating how much memory is being used per MPI process. If you are able to post the full log output (e-mail benv at bcgsc dot ca, or post to a GitHub gist), I could have a look and see ...
written 3 months ago by benv620
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Comment: C: What happened after coverage.hist in Abyss?
... Hi @wangzz, Can you please provide your `abyss-pe` command and your complete log output? It would be helpful determing exactly where the program froze. You can use a GitHub gist for the log output if you don't want to post it here. If possible, please enable verbose logging by adding `v=-v` to yo ...
written 3 months ago by benv620
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Answer: A: Running ABySS at k-mer > 97
... Hi Anand, Glad to hear you were able to get some assemblies running! To answer your questions: * Unfortunately, there is no way to run an assembly with k-mer size > 64 without re-compiling the software. * There is no upper bound for `--enable-maxk`. However: (i) increasing `--enable-maxk` inc ...
written 3 months ago by benv620
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Comment: C: ABySS run problems
... The assembly directory is the working directory for your cluster job, which is usually just the directory where you ran your job submission command (i.e. `sbatch`/`srun`). If you're not sure what directory your job is running in, you can just put a `pwd` command at the top of your job script. I ag ...
written 3 months ago by benv620
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Answer: A: ABySS run problems
... Hi Anand, I'm not sure what the problem is, but I can hopefully provide some hints. It looks like your `abyss-pe` command is correct. I suspect your problems are related your cluster job submission parameters. Learning to run MPI jobs on a cluster usually requires a bit of experimenting with jo ...
written 4 months ago by benv620

Latest awards to benv

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 3 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Scholar 4 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: regenerating -contigs file in ABySS
Appreciated 7 months ago, created a post with more than 5 votes. For A: Reading single-end reads takes forever
Scholar 7 months ago, created an answer that has been accepted. For A: regenerating -contigs file in ABySS
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