Open ailtonpcf opened 5 months ago
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, disk_mb=0, tmpdir=/scratch/qi47rin, partition=standard, qos=normal, time=3-00:00:0
bedtools getfasta -nameOnly -s -fi /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 -bed cache/45-create-eukdetect-db/bed-annotations/fungi--Chromosome--Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic.bed -fo cache/45-create-eukdetect-db/bed-fasta/fungi--Chromosome--Aspergillus_niger_strain_KYF3-tax5061-GCA_029783925.1_ASM2978392v1_genomic.fna
Error: malformed BED entry at line 2. Start was greater than end. Exiting.`
The way I manage was:
awk 'BEGIN {OFS="\\t"} {if ($2 > $3) {print $1, $3, $2, $4, $5, $6} else {print $0}}' input.bed > fixed.bed
Perhaps it might be useful for others.
Do you have by any chance the conda recipe for all the tools required for the database construction?
Bests, Ailton.
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, disk_mb=0, tmpdir=/scratch/qi47rin, partition=standard, qos=normal, time=3-00:00:0
Error: malformed BED entry at line 2. Start was greater than end. Exiting.`
The way I manage was:
awk 'BEGIN {OFS="\\t"} {if ($2 > $3) {print $1, $3, $2, $4, $5, $6} else {print $0}}' input.bed > fixed.bedPerhaps it might be useful for others.
Do you have by any chance the conda recipe for all the tools required for the database construction?
Bests, Ailton.