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Thanks for the pipeline, curious to try it out!
After installing dependencies in a conda environment - Krona, VIBRANT and QUAST databases normally need to be set up and/or updated:
```
Krona inst…
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Hello, I am wondering how can I extract the sequence variant names (named as ASV1, ASV2, ASV3...) together with their sequences from the refseq slot? Is there an easy way to extract the data from the …
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Hello,
I have some ONT reads of _Aspergillus fumigatus_ that I mapped against a reference sequence.
I am using Nanocaller for variants calling, My input files are a BAM file (555,1 Ko; 85 sequen…
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Hostile requires more steps for it to work.
Need to install:
minimap2 (https://github.com/lh3/minimap2)
bowtie2 (https://github.com/BenLangmead/bowtie2)
hostile (https://github.com/bede/hostile)…
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Sir/Ma'am,
I have used metawrap in the past without coming across my current issue, so I do not know what I might be doing wrong. I am getting the following error:
```
[bwa_index] Pack FASTA... […
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Hello,
I have a question about my output. While running through the metaWRAP pipeline we noticed
that we had initial bins (87 concoct, 5 metabat and 7 maxbin) but when we ran bin refinement,
we h…
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Hello, I am trying to align metagenomic sequences, when I run initPipeline with the following command I get the expected output:
`initPipeline -q -1 Unmapped.out.mate1 -d projectDir -i 300:800`
Pr…
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Hi, I caught an error in Process: GAP:MASH_TO_NWK.
```
# .command.err
Command error:
Command 'ps' required by nextflow to collect task metrics cannot be found
# .command.run
nxf_launch()…
lam-c updated
9 months ago
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@fmendezh you mentioned that you were looking for suggestions for easy improvements that could be done with the new pipeline.
[This species page/treatment of species 119349320](https://www.gbif.org…
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Hi, I came across your article recently and I was really interested in understanding the methods you used to generate Figure 6.
I was trying to run your script on my data but I have no clue of how th…