Question: Kronagram from Kraken2 output?
0
gravatar for wolfgang.rumpf
13 days ago by
wolfgang.rumpf10 wrote:

I'm trying to build kronagrams (with KronaTools) from kraken2 output. Has anyone figured out a way of doing this?

kronagram kraken • 93 views
ADD COMMENTlink modified 10 days ago • written 13 days ago by wolfgang.rumpf10

How did you run Kraken2? Can you show a snippet of its output?

ADD REPLYlink written 13 days ago by h.mon25k

I just run Kraken2 from the command line - the output typically looks like this:

> 100.00    15885   0   R   1   root
> 100.00    15885   0   R1  131567    cellular organisms
> 100.00    15885   2   D   2       Bacteria
>  38.89    6177    0   D1  1783272       Terrabacteria group
>  27.10    4305    0   P   1239            Firmicutes
>  21.95    3487    1   C   91061             Bacilli
>  14.16    2250    0   O   186826              Lactobacillales
>   7.90    1255    0   F   1300                  Streptococcaceae
>   7.90    1255    547 G   1301                    Streptococcus
>   4.02    638 429 S   1309                      Streptococcus mutans
>   1.32    209 209 S1  210007                      Streptococcus mutans UA159
>   0.15    24  21  S   1314                      Streptococcus pyogenes
>   0.01    2   0   S1  798299                      Streptococcus pyogenes serotype M59
>   0.01    2   2   S2  798300                        Streptococcus pyogenes MGAS15252
>   0.01    1   0   S1  301449                      Streptococcus pyogenes serotype M5
>   0.01    1   1   S2  160491                        Streptococcus pyogenes str. Manfredo
>   0.06    10  10  S   2420310                   Streptococcus sp. FDAARGOS_522
>   0.06    10  7   S   1311                      Streptococcus agalactiae
>   0.01    2   2   S1  1309807                     Streptococcus agalactiae ILRI005
>   0.01    1   1   S1  1203670                     Streptococcus agalactiae GD201008-001
>   0.03    5   0   S   1348                      Streptococcus parauberis
>   0.03    5   5   S1  873447                      Streptococcus parauberis NCFD 2020
>   0.03    4   0   G1  119603                    Streptococcus dysgalactiae group
>   0.02    3   0   S   1334                        Streptococcus dysgalactiae
>   0.02    3   2   S1  119602                        Streptococcus dysgalactiae subsp. equisimilis
>   0.01    1   1   S2  759913                          Streptococcus dysgalactiae subsp. equisimilis AC-2713
>   0.01    1   1   S   1336                        Streptococcus equi
>   0.03    4   4   S   82348                     Streptococcus pluranimalium
>   0.02    3   0   G1  671232                    Streptococcus anginosus group
>   0.02    3   0   S   1338                        Streptococcus intermedius
>   0.02    3   3   S1  862966                        Streptococcus intermedius C270
>   0.01    2   2   S   1346                      Streptococcus iniae
>   0.01    2   1   S   1307                      Streptococcus suis
>   0.01    1   1   S1  1340847                     Streptococcus suis T15
>   0.01    2   2   S   2420308                   Streptococcus sp. FDAARGOS_520
>   0.01    2   0   S   1313                      Streptococcus pneumoniae
>   0.01    2   2   S1  869311                      Streptococcus pneumoniae SPN032672
>   0.01    1   1   S   1814128                   Streptococcus halotolerans
>   0.01    1   1   S   2173853                   Streptococcus sp. Z15
>   5.06    803 0   F   33958                 Lactobacillaceae
>   5.06    803 174 G   1578                    Lactobacillus
>   3.88    617 0   S   1596                      Lactobacillus gasseri
>   3.88    617 617 S1  324831                      Lactobacillus gasseri ATCC 33323 = JCM 1131
>   0.01    2   2   S   33959                     Lactobacillus johnsonii
>   0.01    2   0   S   1584                      Lactobacillus delbrueckii
>   0.01    1   1   S1  29397                       Lactobacillus delbrueckii subsp. lactis
>   0.01    1   1   S1  83684                       Lactobacillus delbrueckii subsp. delbrueckii
>   0.01    2   1   S   1587                      Lactobacillus helveticus
>   0.01    1   1   S1  767462                      Lactobacillus helveticus H10
>   0.01    2   2   S   1590                      Lactobacillus plantarum
>   0.01    1   1   S   1622                      Lactobacillus murinus
>   0.01    1   1   S   1598                      Lactobacillus reuteri
>   0.01    1   1   S   53444                     Lactobacillus lindneri
>   0.01    1   1   S   1720083                   Lactobacillus sp. HSLZ-75
>   1.20    191 1   F   81852                 Enterococcaceae
>   1.20    190 0   G   1350                    Enterococcus
>   1.20    190 184 S   1351                      Enterococcus faecalis
>   0.04    6   6   S1  565651                      Enterococcus faecalis ARO1/DG
>   0.01    1   0   F   18682
ADD REPLYlink modified 12 days ago • written 12 days ago by wolfgang.rumpf10

Possible duplicate of Transforming kraken outputs to krona ?

ADD REPLYlink written 12 days ago by harish200
1
gravatar for wolfgang.rumpf
10 days ago by
wolfgang.rumpf10 wrote:

As it turns out the easiest solution was to use the raw kraken2 output (which normally gets dumped to standard out) and pipe that to the latest version of recentrifuge (0.28.9), which generates lovely kronagrams.

ADD COMMENTlink written 10 days ago by wolfgang.rumpf10

Glad to know that it worked!

ADD REPLYlink written 10 days ago by harish200
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