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Hi, I am stuck at the assembly stage of a ~450 Mb genome using canu version 1.4. Here is the original command:
```
canu -p cargold -d cargold.out genomeSize=450m -pacbio-raw ../20170*/*/Analysis_Re…
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I'm getting 'INVALID OVERLAP' messages from canu when running read correction on RNASeq files with minimap2. Here's one of the outputs:
```
$ cat mmap.000015.out
Running job 15 based on command…
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Hi.
Can we add assembly contig of NGS to canu input to reduce pacbio coverage requirement?
most of contig of NGS are less than 100K. and we can use them as pacbio reads?
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We have encountered another place where the $PBS_O_WORKDIR is not being properly expanded. This is towards the end of the correction phase when it is building the .gkpStore. The referencing to the ovl…
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Given that canu commonly only deal with longest reads up to 40x coverage, I wonder how canu can be used in long amplicon assembly.
For example, I would like to amplify and sequence (use nanopore) a…
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Hi, I'm not sure if this question should be posted here, so please direct me to the correct place if needed.
I'm running Canu release v1.5 on a cluster of 5 AWS EC2 instances with ubuntu 14.04, eac…
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Here is the error log:
```
-- Detected Java(TM) Runtime Environment '1.8.0_45' (from '/common/opt/jdk1.8.0_45/bin/java').
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image …
qslin updated
7 years ago
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On our HPC we have are using PBSPro_13.0.2.153173 as our scheduling system and we run into some submission errors when trying to run on the sample data.
1. PBS does not recognize the flag `-d working…
timeu updated
7 years ago
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Hi,
Got an issue trying to use CANU. I'm a novice user, so it could be all me. Output from the OSC GRID is below. Attached is the CANU error log (wf.gkpStore.err).
Running on GRID (Ohio Sup…
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An interesting error during mhap, I suspect it is due to an i/o blocking issue on our lustre file system. This results in only a couple of jobs failing, but that's enough to break things. Running this…