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Hi Matin,
when I run GECCO on the Lactobacillus_delbrueckii example dataset with `bgcflow run`, I get this error:
`/usr/bin/bash: line 2: 657128 Illegal instruction (core dumped) gecco run --g…
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I attached the output while trying to generate a genome graph...
Any suggestion would be appreciated!
[M::main::0.001*4.79] loaded the graph from "bap1_hg38.fa"
[M::mg_index::0.004*1.46] indexed th…
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I would like to use the pipeline on a large plant genome. Would it be to run separately on chromosomes or directly on the entire genome? Are there any requirements for CPUs and RAM? Have you ever test…
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Hi,
I'm having issues trying to run SigProfiler for CNV data using custom CNV calls. We have an in-house pipeline for CNV calls that is similar to the ASCAT approach, tailored to our WGS data. I t…
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Dear all,
I recently tested scripts in 4-Assembly folder and found what needs to be fixed.
1. runpipeline.sh
cp $core_genome ${output_dir}/core_assembly/step0_assembly/ .
core_genome_file=${ou…
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Thank you for suggesting `--skip_clonalframe` in
https://github.com/bactopia/bactopia/issues/100
In [Bactopia Tools - pirate](https://bactopia.github.io/bactopia-tools/pirate/), [Input for Clona…
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gridss conda installation
jar file 2.13.2-gridss-jar-with-dependencies.jar
platform : Ubuntu 22
The code I ran
`gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gri…
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**Hello!
I am receiving the following error:**
EOFError: EOF when reading a line
/var/spool/slurm/slurmd/job9943744/slurm_script: line 27: --probefile: command not found
**with the followi…
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Hi, I used bambu on one sample. The alignment result(.bam) of this sample is about 34G. And I run bambu on HPC cluster. I set the cpu number to 20. Then run it. But it took 6 hours to finish the job. …
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Hello Torsten,
I wanted to see how much difference does it make to use different alignment strategies for my generated phylogeny (I've used core gene alignment from Roary before). However, default…