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We've never had tests for Launchers other than local because deploying PBS/SGE/etc. on CI has never been feasible.
But in our new containerized world, I think it *should* be feasible to run batch s…
minrk updated
3 years ago
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Hello,
I trying to use on a hpc Canu -correct to correct Nanopore raw reads. I ahve installed Canu via Conda (with gnuplot). The submitted job end without error message but generate no fasta.gz corre…
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## Description of the problem
I'm running into the following error when trying to run the pipeline on the tiny demo dataset, and unfortunately I do not get why the process always stops. The command…
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**Description**
When executing the pipeline with command:
bactopia --fastqs fastqs.txt --datasets datasets/ --species "Escherichia coli" --coverage 20 --outdir local_bactopia_farm --cpus 4
proce…
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Hello, again Francisco!
So after the extractProteinbins step, I had 93 .faa files. I ran the 'bash metaGEM.sh -t carveme -j 93 -c 4 -m 20 -h 4' command after this and ended up with only 47 models i…
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I plan to use interproscan on a Slurm cluster and I'll be editing the interproscan.properties to work on it. I can submit a pull request with the interproscan.properties edited to include those change…
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Hi,
Using Windows I'm running frequently into errors while using the terminal. This happened with both the release version of RStudio IDE (1.1.423) and the latest daily build (1.2.350) from https:/…
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Hi,
I'm trying to run the example dataset. (snakemake `5.19.2` ) My server crashed during the workflow and I tried to re-run it.
```
$ ./run.bash --sge-cluster && echo OK
$
```
this the th…
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**Describe the bug**
A sample that contains fastqs from multiple lanes and libraries is failing at the MarkDuplicates step:
`Exception in thread "main" htsjdk.samtools.SAMException: Value was put …
tgebo updated
3 years ago
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**Hi, I am trying to create my index with phyloflash but error messages appear when clustering. I could see that other people had this problem but I could not fix it by looking at the advice given for…