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Hello,
I am having trouble with the mikado serialize step. I get this error every time:
mikado serialise --json-conf configuration.yaml --xml mikado_prepared.blast.tsv --orfs mikado.orfs.gff3 --j…
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* ribotricer version: 1.3.3
* Operating System: Linux
### Description
Just experimenting with `--stranded`
### What I Did
```
ribotricer detect-orfs \
--bam SRX11780888_chr20.bam \
…
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Having an issue with the hmmscan part of the run
```
Some tasks failed![dammit.annotate:ERROR]
TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR]
Command error: 'cat…
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Is the pdk accurate enough? Since a7 v t7 has around 50% differences in synthesis by my experimental trial.
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Hello,
I saw that pyrodigal can use different translation tables (issue #34), which is great!
Do you know if pyrodigal can correctly identify selenocysteine insertions? (And pyrrolysine too)
I …
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Hello,
I wanted to know if DiversiTools with ORFs supports genes in the minus strand of the reference sequences. If so, how should they be identified in the Coding.regions files? I noticed that in …
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We would like the ability to provide a gff formatted file of ORFS and have results filtered so that only those misassemblies which overlap orfs are reported.
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Sometimes the lengths of the predicted nt & aa ORFs do not match up. If this is the case the nt-ORFs appear to be a bit longer (2-3 codons).
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Hello all!
I would like to report a issue in the first step of VirClust analysis. The first step (step1A) is the orf prediction and we have obtained an error issue for this step with a multifasta fi…
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Good morning
I am using the command ./MEGAN +g -x "import blastfile= assembly.orfs.hmm.blast.xml meganfile=temp.rma;recompute toppercent=5;recompute minsupport=1;update;collapse rank=Species;update;se…