I can not get fasta file with the hit sequences running barrnap
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4 weeks ago
pavelasquezv ▴ 10

Hi all!

I hope you are well,

I can get the fasta file running barrnap. This is the code:

barrnap --kingdom bac --outseq ecoli__ref_rrna.fa GCF_000005845.2_ASM584v2_genomic.fna > ecoli_ref_rrna.gff

more information in the google colab

The results is the following. I think the problem is

GCF_000005845.2_ASM584v2_genomic.fna' -bed '/tmp/nFt7IpApWZ'  ERROR: Unrecognized parameter: -name+

Please, let me know if you can help me.

Many thanks

`[barrnap] This is barrnap 0.9
[barrnap] Written by Torsten Seemann
[barrnap] Obtained from https://github.com/tseemann/barrnap
[barrnap] Detected operating system: linux
[barrnap] Adding /usr/local/lib/barrnap/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /usr/local/bin/nhmmer
[barrnap] Found bedtools - /usr/local/bin/bedtools
[barrnap] Will use 1 threads
[barrnap] Setting evalue cutoff to 1e-06
[barrnap] Will tag genes < 0.8 of expected length.
[barrnap] Will reject genes < 0.25 of expected length.
[barrnap] Using database: /usr/local/lib/barrnap/bin/../db/bac.hmm
[barrnap] Scanning GCF_000005845.2_ASM584v2_genomic.fna for bac rRNA genes... please wait
[barrnap] Command: nhmmer --cpu 1 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/usr/local/lib/barrnap/bin/../db/bac.hmm' 'GCF_000005845.2_ASM584v2_genomic.fna'
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 3427222..3428759 - 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 2729617..2731154 - 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 4035534..4037071 + 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 4166662..4168199 + 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 4208150..4209687 + 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 223774..225311 + 16S ribosomal RNA
[barrnap] Found: 16S_rRNA NC_000913.3 L=1538/1585 3941811..3943348 + 16S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 225761..228661 + 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 4168643..4171543 + 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 2726282..2729182 - 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 4210045..4212945 + 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2902/3232 4037521..4040422 + 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 3943706..3946606 + 23S ribosomal RNA
[barrnap] Found: 23S_rRNA NC_000913.3 L=2901/3232 3423881..3426781 - 23S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 228760..228870 + 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 3946704..3946814 + 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 2726074..2726184 - 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 3423673..3423783 - 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 4040521..4040631 + 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 3423428..3423538 - 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 4171641..4171751 + 5S ribosomal RNA
[barrnap] Found: 5S_rRNA NC_000913.3 L=111/119 4213044..4213154 + 5S ribosomal RNA
[barrnap] Found 22 ribosomal RNA features.
[barrnap] Sorting features and outputting GFF3...
[barrnap] Writing hit sequences to: ecoli__ref_rrna.fa
[barrnap] Running: bedtools getfasta -s -name+ -fo 'ecoli__ref_rrna.fa' -fi **'GCF_000005845.2_ASM584v2_genomic.fna' -bed '/tmp/nFt7IpApWZ'
*****ERROR: Unrecognized parameter: -name+ *******


Tool:    bedtools getfasta (aka fastaFromBed)
Version: v2.26.0
Summary: Extract DNA sequences from a fasta file based on feature coordinates.

Usage:   bedtools getfasta [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>

Options: 
    -fi Input FASTA file
    -bed    BED/GFF/VCF file of ranges to extract from -fi
    -name   Use the name field for the FASTA header
    -split  given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
    -tab    Write output in TAB delimited format.
        - Default is FASTA format.

    -s  Force strandedness. If the feature occupies the antisense,
        strand, the sequence will be reverse complemented.
        - By default, strand information is ignored.

    -fullHeader Use full fasta header.
        - By default, only the word before the first space or tab is used.

[barrnap] Done.`
barrnap bed • 121 views
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