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I have an assembly of the NA12878 human reference sample in GFA format. Running `vg view` to convert to a `.vg` file runs to completion (albeit using >300GB RAM) but the resulting file appears to be i…
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The 2.0.3 release now optionally depends on pigz (I am assuming http://www.zlib.net/pigz/) and zsh (do you really mean https://www.zsh.org ?).
Has the documentation been updated to cope with the fo…
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I wasn't able to get my patched Powerline fonts to show up in iTerm so I decided to give `nerd-fonts` a go. I can't get the defaults to change, no matter what I do.
Here is my `.zshrc` file:
`…
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I am trying to use our big memory node on our cluster as if it were a local node. To do that I need to submit the canu string as a (pbs_pro) job but configured to run run as a local job. The job start…
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Hi
I am running a canu (1.7) assembly of a plant genome (1.3gb) based on 11x PacBio reads. It all goes well till unitigging, when bogart fails with a segmentation fault.
I tried restarting and then …
ovidp updated
6 years ago
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This is the error information:
#5: Unexpected value found! Overlaps are not formatted in the PAF format. Exiting.In function: 'ParsePAF'.
And my paf file looks like:
m170110_073744_42228_c1011365…
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Hello,
After having ran minimap/miniasm on ~55x of PacBio data, I used Racon and ended with the following error:
```
bin/racon -v 9 -t 16 filtered_subreads.fastq.gz 14smrt.paf 14smrt.gfa racon1…
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I used canu1.6 for assembly a ~15Mb genome.
It seems stack at the trimming step, which has been running for 3 days already (12 cores, 90GB memories).
I re-ran the trimming and it still stuck in the…
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Hello Sergey,
My canu run doesn't output genome assembly. It only generated correction folder. It seems to me that trim and assemble were aborted, but no error was thrown in the log file.
This…
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Hi,
I use canu 1.6 (Linux, single machine) to assemble a mammalian genome. I perform each of the three steps individually and noticed that the 3rd step (assemble) uses the corrected reads although …