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Hello, I need help in interpreting abricate (vfdb) result.
Based on result below can I assume that there is hilA gene in the analyzed strain? I mean if I can sum coverage results for these fragments …
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### Description of the bug
Hi @GallVp ,
The assemblyQC pipeline failed on a set of transcriptome assemblies. The .nextflow.log ended with _DEBUG nextflow.script.ScriptRunner - > Execution complet…
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Add a plot which lets you view the
y: proportion of cDNA (alternatively the RPKM)
x: gDNA
fit a regression line across and find things which are 2 SDs away from the regression
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I was just wondering what might explain this....I have some spades assembled WGS sequences and I used the contigs as input for ngmaster. I upload the same contigs to pubmlst and get completely differe…
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Hi VIni,
I keep getting this error message:
[Sat Jul 13 01:49:37 2024]
Error in rule concatenate_contigs:
jobid: 56
input: output/assembly/megahit/coassembly/coassembly.contigs_rename…
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Currently, the way my pipeline works is that it outputs a bam for the spike-in controls, and another for the genomic contigs. Due to this, I cannot run scan_genomic_contigs() because if I run on only …
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Hello,
When I try to run cobra, I just get error message like this
```
(cobra) wk@t:~/res/20240905_cobra$ cobra-meta -f /home/wk/res/test/SPAdes/contigs.fasta -q /home/wk/res/20240905_cobra/metaSp…
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Hi,
I used VirSorter v2.1 on contigs from environmental metagenomes. I selected potential viral contigs with score >0.8. I then verify completeness with checkV. Several potential viral contigs whe…
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Hey there!
In some cases I experience a never ending loop of Begin Extensions / Fuse contigs:
```
0:12:03 Begin Extensions
0:12:08 Fuse contigs
0:12:08 Begin Extensions
0:12:13 Fuse contigs
…
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I tried to run configureStrelkaSomaticWorkflow.py for the WGS BAM files. But got an error:
CONFIGURATION ERROR:
'normal' BAM/CRAM file is missing reference fasta chromosome: 'hs37d5'
I guess that …