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Hello guys, I am trying to run the tutorial to check if the installation was correct (and while I am waiting for the real data to run on it).
First, I noticed that if I don´t specify "--outdir" he…
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Dear All,
I would like to report some errors arisen while I was running 6 instances of GapSeq in my HPC cluster. In each instance that was the error output:
```
Warning: [tblastn] Query_1 UniRef5…
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Hey,
I'm trying to run gtotree on a linux cluster but i'm getting some strange errors. For the majority of genomes, when searching for the target genes, the operation is aborted and I get the foll…
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I would like to conduct a gene gain and loss analysis in my bacterial species of interest, for that I intended to use your CAFE tool. However, my literature survey concluded that, CAFE tool has been u…
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HI, I am trying to make the database from source using the make_databses.pl. But, I am confused about why there is a need to download the preformatted database file as shown in the make _databses.pl …
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Hi Donovan,
I suspect you are aware of this issue but I wanted to ask. Currently CheckM underestimates completeness of many genomes from the CPR/Patescibacteria which lack many SGCs found in most …
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Hi,
I have been using PIRATE for bacterial genomes and was wondering if there is a way to conduct an analysis by adding more genomes to an old run.
I used it on 130 genomes in the first run and now…
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@lindseyfaye @rsmoak, let's put together the results we have so far into a PPT format. Perhaps one slide per result + any key method information. I'm currently working on the OrthoMCL results, and pla…
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Is there a way to start the analysis after ORF calling step?
If doing ORF calling with prodigal, does it use the "-c" option, I'm asking since it is not recommended for meta-genomics data.
As for th…
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Dear CARD RGI developer team,
I have taken different bacterial species to make json file by use RGI command offline .
I use the command
`rgi -t protein -i salmonella.fasta -o salmonellaprot.JSON…