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For StrainPro v0.9.2, it appears that when calling `StrainPro-build`, that executable requires `StrainPro-rep` to be located at `bin/StrainPro-rep` relative to the user's current working directory. T…
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When I run updateAccessions.sh (both locally and on an HPC server) i get this error message: "Update failed. Is your internet connection okay?".
I tried to download accession files to add them manual…
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Hi,
I think your module about bin refinement is perfect. I concatenated forward and reverse reads to assembly and bin in other software.
May I please know can I use it with single ended? Since the…
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Hi again! My supervisor and I have been troubleshooting our efforts to update the GTDB_release207 pre-made custom database with a selection of genomes from JGI GOLD (see previous issue #29). Based on …
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I just cloned the most recent version of StrainPro yesterday. I'm running Strainpro-build on the example "ecoli.fa" file with freshly downloaded taxdump files. The build job has been running for ~15 h…
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This situation applies in an HPC environment and there are multiple concurrent jobs running which are calling ETE3 independently and there has either been an update to the NCBI database or momentary c…
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Hello,
I'm trying to create a Diamond reference database for the Uniprot reference proteomes, but the instructions I found for the older version of BlobTools (https://blobtools.readme.io/docs/taxon…
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Hi,
I just ran the Blobtoolkit pipeline.
Thanks for the great tool.
I have something weird with my genome is that most of my contigs (more than 95%) have no hits. I am working on a Mollusc and…
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Hello! I am getting this issue when installing the databases using this command:
command: /home/delaney/miniconda3/bin/krakenuniq-download --db DBDIR --threads 10 --dust refseq/bacteria refseq/ar…
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#### Description
Issue /CSCfi/metadata-submitter-frontend/issues/418 requires an API to call, however NCBI does not provide an easy way to query their API and for this we need to construct our ow…