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Good day,
I get this error when trying to run the pipeline on the example fastqs (I get the same error on my own fastqs as well):
"(transflow) [jloubser@khaos transflow]$ bash transflow.sh --conf…
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In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits …
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It seems if GOTTCHA fails to find anything, then the temp folder remains after the run is complete. Everything _seems_ to of fine, but this makes me wonder if the tool carried out the analysis correct…
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Dear Roary author and support team:
I use a RHEL 7.9 server to test Roary container.
I use command 'docker pull sangerpathogens/roary' to acquire an image "docker.io/sangerpathogens/roary "
In…
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While exccuting the roary pipeline, I had this error:
`
(roary) |09:51:44|jflucier@ip29:[roary]> roary -p 12 prokka_ann/13401/*.gff -cd 80 -f roary_ann/13401
Use of uninitialized value in requir…
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Suggestions provided by @haruosuz
- bactopia can accept GFF3 files (.gff) instead of FASTA files (.fna) as input, like PIRATE and Roary, to skip Prokka?
- bactopia can do alignment trimming (e.g. …
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Hi!
I'm trying to build a pangenome using Roary. However, I got some strange outputs and some warning.
**The code I ran:**
**(Roary) login-2:roary$ roary -p 128 *.gff -i 90 -cd 95 -f roary_out…
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## Short description of the problem
Attempting to generate DAG diagrams with `anvi-run-workflow --save-workflow-graph` results in an error due to pulp v2.8.0 which installs with anvi'o v8.
## an…
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Would it be possible to handle ambiguous reference bases properly? That would increase the alignment quality for viral use cases.
Thank you.
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I am having this problem using the SAM file to identify the off-target
python ~/bin/guideseq-1.0.2/guideseq/guideseq.py identify --aligned ~/Desktop/WORKS/CODE/download/AA_1.sam --target_sequence c…