-
http://oyster-river-protocol.readthedocs.io/en/master/
-
Hello,
I have installed ORP according to the instructions but when running the 'Test the installation' section in the 'sampledata' folder I get this error:
Total time = 2.32095s
Reported 69 pair…
mb492 updated
5 years ago
-
Hi @macmanes I'm trying to run orthofuser.mk on a set of transcriptomes (same species) that have been generated using the Oyster River Protocol (ORP). I'm running a docker container that has the most …
-
Here is the CMD output:
```
CHECKPOINT: Unitig assembly completed.
CMD: bash -euo pipefail -c 'abyss-pe graph=adj --directory=/home/orp/Oyster_River_Protocol/DATA/assemblies/SRR5330501.transabyss…
-
oyster.mk main fails on the test data set with the following error. Quick google search reveals similar errors in conda, sometimes reported fixed by using newer Python.
======= SPAdes pipeline fi…
-
I launch the following command:
/home/orp/Oyster_River_Protocol/oyster.mk main STRAND=RF TPM_FILT=1 MEM=400 CPU=64 READ1=concatenated_R1.normalized.trimmed.fq R2=concatenated_R2.normalized.trimmed.…
-
Hello!
Great tool. I have heard a lot about it before tried to use. I went by conda-way, just installing all dependencies described in recipe. But every attempt to run the transrate lead me to the er…
-
Hi Mathew,
I'm finally ready to give it a go to your pipeline. I have a few questions to ask you first, some regarding the installation and some other to the usage.
Re installation:
1) Is the…
-
Hi,
I am having this SNP error (I found this in the sanp.log file) when I ran Transrate on a large dataset.
```
Loading index from directory... 0s. 193003239 bases, seed size 23
Aligning.
W…
-
I Installed boostlib and exported LIB path in .bashrc and configured BInPacker with boost lib it went well. make pops up an error. How do I rectify this?
./configure --with-boost=/home/softwares/boos…