ailtonpcf

files with different read lenght

1

Is there a way to run many samples with different read length?

squeue cmd not found when running R targets on singularity docker image

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To whom it may concern, Thank you for the templates to use on HPC :D I'm triggering an R target pipeline on snakemake together with R docker image on singularity....

Can't use k of 39 (must be <= 31)

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Hey, I would like to try Krakenuniq with kmers longer than 31, however I get an error: `Can't use k of 39 (must be

invalid escape sequence '\d' on get_uncomputed_taxid_per_busco

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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,...