nhartwic
nhartwic
Apologies for the delay on this. Got sidetracked. [EtweTM011.v2.15593.fasta.gz](https://github.com/oushujun/EDTA/files/8544264/EtweTM011.v2.15593.fasta.gz) [EtweTM011.v2.fasta.mod.EDTA.TElib.fa.gz](https://github.com/oushujun/EDTA/files/8544265/EtweTM011.v2.fasta.mod.EDTA.TElib.fa.gz) Here is the contig and the repeat library that EDTA generated for whole assembly.
Ok... Took longer to update than I'd hoped. Some stuff got sidetracked. I'm now running on Snakemake 7.9.0 and tibanna 1.9.2 and can confirm that the bug is still present....
You do not need a different transcriptome for each readset. Your general workflow should be... 1. prepare a transcriptome in fasta format 2. For each sample, align that sample to...
Any progress or expected time when separation of I/O will be implemented? I don't think I can include tombo in any generalized pipelines until this issue is resolved.
It is useful in that it represents how much of your dataset isn't in any of the columns you are currently looking at. In terms of what it would look...
In my case, the issue was my python version was too new. Upgrading didn't resolve the plot_metrics issue. Here is a new plot_metrics output... https://salk-tm-logs.s3.amazonaws.com/aA6bccyAeLQt.metrics/metrics.html [job log](https://github.com/4dn-dcic/tibanna/files/9192025/job.aA6bccyAeLQt.log) [top log](https://github.com/4dn-dcic/tibanna/files/9192026/job.aA6bccyAeLQt.top.log)
Ok, this job ran for an hour: https://salk-tm-logs.s3.amazonaws.com/eTcBZv8sWlB8.metrics/metrics.html ...Here are all the "log_files" that were uploaed to s3 and are associated with the job... [job_eTcBZv8sWlB8.tar.gz](https://github.com/4dn-dcic/tibanna/files/9193659/job_eTcBZv8sWlB8.tar.gz) ...Cloudwatch logs associated with the...
Not 100% sure what you are referring to but I don't think I use GCAP/4DN. I assume tibanna uses some specific image when spinning up ec2 instances that includes tibanna...
It is possible there are multiple issues happening here. I haven't seen complete metrics on any of my jobs that I've checked. I'm not sure how many I've checked, but...
I'm more referencing the potential issues with requesting more compute than your account has available on quota. Plot_metrics is great for determining how many cores are actually being used by...