EukDetect
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allind
Hi, is it possible to get an updated database at some point in the near future? Or is there a way how to update/create a database by ourselves? Thanks in...
Hello thanks for developing this interesting tool! I'm preparing a meta-analysis, and I wanted to explore the eukaryotic component of the microbiome with EukDetect. However, after reviewing the documentation and...
Hello, Thanks for creating this pipeline! Unofrtunately, I have issues getting it to run on HPC environment (Slurm). Snakemake scripts are unable to find packages that were installed using conda:...
I have my reads stored in bam-files and need to convert them to fastq before running EukDetect. I have to convert one-by-one since I a lot of input files and...
Hey @allind I tried to install eukdetect but when I want download EukDetect database from Figshare: (run this command): wget https://ndownloader.figshare.com/files/34885596 it gave an error saying: Connecting to ndownloader.figshare.com (ndownloader.figshare.com)|54.217.124.219|:443......
Hi @allind: Thanks for the quick reply! I try directly downloading the database (most recent is version 9) from this link: https://figshare.com/articles/dataset/Eukdetect_database/12670856 However,when I run: tar -zxvf 12670856 , it...
Dear Dr. Lind, I'm generating a custom eukdetect db and I'm stucked at get_uncomputed_taxid_per_busco.py. It fails with the following message: """ python /home/qi47rin/proj/00-git/EukDetect/build_db/get_uncomputed_taxid_per_busco.py --speciestax cache/45-create-eukdetect-db/genomes-table/species_taxid.tsv --fasta cache/45-create-eukdetect-db/genes-repeat-filtered/buscos_cdhit99_less10perc_repeats_masked.fna --collapsed_ids cache/45-create-eukdetect-db/busco-cdhit99-renamed/buscos_cdhit99_renamed_busco_seqid_sequential_correspondence.txt --taxdb...
Dear Dr. Lind, I'm currently experiencing issues with bedtools getfasta: `rule from_bed_to_fasta: input: cache/45-create-eukdetect-db/from-tbl-to-bed.done, /work/qi47rin/proj/02-compost-microbes/cache/28-kuniq-all-kings-db-not-masked/all-kingdoms-genome/library/fungi/Chromosome/Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic.fna output: cache/45-create-eukdetect-db/bed-fasta/fungi--Chromosome--Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic.fna jobid: 0 reason: Missing output files: cache/45-create-eukdetect-db/bed-fasta/fungi--Chromosome--Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic.fna wildcards: KINGDOM=fungi, LEVEL=Chromosome, GENOME=Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic resources: mem_mb=10000,...