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I am trying to assemble a viral genome after correction of the Pacbio long sequences by Illumina short reads using LoRDEC. During the assembly, I have gotten an error such as 'Bogart failed'. Could yo…
tay45 updated
6 years ago
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Hello, I am currently trying to run canu with the ecoli test data.
Unfortunately, the run doesn't seem not going through properly. Even though I wrote the exact sampe example code, I found from the t…
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Hi,
1) Is Orthofinder suitable for microbial genomes?
2) I have run orthofinder on 15 microbial genomes and I am getting the following error using iqtree or fasttree. see below:
Multiple potent…
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I am trying to run the squashed option in Canu. And when I get to the unitigging step, I get errors in 2 overlap jobs.
Canu script for job submission in PBSPro
```
#!/bin/bash
#PBS -P RDS-FAE-OS…
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Hi, anybody would help me?
I have a problem with canu. I build a bash file, then I use "qsub" command to submit this task to our server. It always fails "Mhap overlap jobs failed, tried 2 times, givi…
KSL22 updated
6 years ago
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I've assembled the sequence step by step, and I have an issue at the second trim. error rate=0.039 command was successful complete. So, I don't know why this command couldn't run. Thank you
```
ca…
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I'm having trouble getting CANU to run. I'm working under Linux using
CANU v1.7 (binary distribution):
```
canu --version
Canu 1.7
```
The command I'm running is this:
```
/canu-1.7/Li…
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Hi, I hope your help. I ran on a Linux server. This is the command I used with the feedback it printed.\
I know that I could use option gnuplotTested=true to continue the program. But I want these pl…
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Hi,
I'm trying to assemble some amplicon sequencing data, but I keep getting the exit code 139. The amplicon is only ~700bp long, and I'm running this in an Ubuntu 16.04 virtual environment. The co…
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Do you have an idea of what may have happened during the mhap step? I've rerun this a couple of times with the same error message.
```
cd correction/1-overlapper
./mhap.sh 69 > ./mhap.000…