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lindyguo

bracken_plot's Issues

Plot not generated

Hello acvill,
I have tried to run bracken_plot, however no plot is being generated.
image
image

I am getting this outcome.

Please look into this.

With regrads,
In2S

Is it possible to use it to plot krakenuniq outputs too

here is how a krakenuniq report looks like

# KrakenUniq v1.0.3 DATE:2023-08-06T00:57:24Z DB:/gss/work/asga9989/krakenuniq/microbial-nt DB_SIZE:706079654188 WD:/gss/work/asga9989/all_samples_run
# CL:/cm/shared/uniol/software/8.3/KrakenUniq/1.0.3-intel-2019b/bin/krakenuniq --db /gss/work/asga9989/krakenuniq/microbial-nt --threads 20 --fastq-input --gzip-compressed --paired --output 07_TAXONOMY_references_removed/_PL17_99indbel.krakenuniq --report-file 07_TAXONOMY_references_removed/_PL17_99indbel-krakenuniq-report.tsv 01_QC/_PL17_99indbel-FILTERED_R1.fastq.gz 01_QC/_PL17_99indbel-FILTERED_R2.fastq.gz
%       reads   taxReads        kmers   dup     cov     taxID   rank    taxName
43.16   783047  783047  132171775       3.13    NA      0       no rank unclassified
56.84   1031262 3084    504258  49.4    8.57e-06        1       no rank root
56.47   1024531 4231    491054  20.4    8.674e-06       131567  no rank   cellular organisms
54.03   980284  199152  475276  13.8    1.16e-05        2       superkingdom        Bacteria
31.88   578351  139858  424790  6.27    2.301e-05       1224    phylum        Pseudomonadota
12.22   221695  129781  337596  4.34    3.528e-05       1236    class           Gammaproteobacteria
3.011   54630   7       1869    62.1    7.733e-07       91347   order             Enterobacterales

Taxonomy IDs not matching for species XXX: (216819 190338)

Dear bracken_plot development team,

One error occurred during processing Family and Genus level files.

Processing Output File 1_F_nt.bracken:: Sample 3
Taxonomy IDs not matching for species Xylophagaidae: (92613 183505)
PROGRAM START TIME: 02-02-2023 21:27:09
Processing Output File 10_G_nt.bracken:: Sample 1
Taxonomy IDs not matching for species Cyclophora: (216819 190338)
PROGRAM START TIME: 02-02-2023 21:27:09

Do you have any idea how to deal with this problem?

Best,

Bing

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