Custom LCA with custom Lineages

[mr-eyes]

I have a custom sourmash-LCA-friendly lineages as described here. I created custom lineages for my tree that does not follow the identifiers,superkingdom,phylum,class,order,family,genus,species,strain naming convention. Is there a way to make sourmash works on that without throwing

Building LCA database with ksize=51 scaled=10000 moltype=DNA.
examining spreadsheet headers...
** assuming column 'Leaf_ID' is identifiers in spreadsheet
** assuming column 'level_0' is superkingdom in spreadsheet
** assuming column 'level_1' is phylum in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain

---

Leaf_ID,level_0,level_1,level_2,level_3,level_4,level_5,level_6,level_7,level_8,level_9,level_10,level_11,level_12,level_13,level_14,level_15,level_16,level_17,level_18,level_19,level_20,level_21,level_22,level_23,level_24,level_25,level_26,level_27,level_28,level_29,level_30,level_31,level_32,level_33,level_34,level_35,level_36,level_37,level_38,level_39,level_40,level_41,level_42,level_43,level_44,level_45,level_46,level_47,level_48,level_49,level_50,level_51,level_52
SRR13739007,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,node_15,node_16,node_17,node_18,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13738983,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,node_15,node_16,node_17,node_18,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739027,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,node_15,node_16,node_17,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13738996,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,node_15,node_16,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739025,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,node_15,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739019,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,node_14,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739024,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,node_13,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739021,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,node_12,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739016,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,node_11,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739017,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,node_10,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739018,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,node_9,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739026,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,node_8,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739078,node_0,node_1,node_2,node_3,node_4,node_5,node_6,node_7,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na
SRR13739020,node_0,node_1,node_2,node_3,node_4,node_5,node_6,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na,na

[mr-eyes]

Seems to work after -f for force.

! sourmash lca index -k 51 --scaled 10000 -f {output_tsv} {output_newick}.lca.json --from-file {lca_sigs}

[mr-eyes]

No. I was wrong. The command didn't terminate with -f however the indexing is wrong.

Building LCA database with ksize=51 scaled=10000 moltype=DNA.
examining spreadsheet headers...
** assuming column 'Leaf_ID' is identifiers in spreadsheet
** assuming column 'level_0' is superkingdom in spreadsheet
** assuming column 'level_1' is phylum in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_2' is class in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_3' is order in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_4' is family in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_5' is genus in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_6' is species in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
** assuming column 'level_7' is strain in spreadsheet
whoa, too many assumptions. are the headers right?
expecting identifiers,superkingdom,phylum,class,order,family,genus,species,strain
...continue, because --force was specified.
737 distinct identities in spreadsheet out of 737 rows.
56 distinct lineages in spreadsheet out of 737 rows.
... loaded 737 signatures.907 (737 of 737); skipped 0 so farr
loaded 12386552 hashes at ksize=51 scaled=10000
56 assigned lineages out of 56 distinct lineages in spreadsheet.
737 identifiers used out of 737 distinct identifiers in spreadsheet.

And when query:

finding query signatures...
outputting classifications to -
ID,status,superkingdom,phylum,class,order,family,genus,species,strain
SRR8614047,found,node_0,node_1,node_2,node_177,node_178,node_179,node_257,node_346
classified 1 signatures total

So basically, it ignored my custom taxonomy levels.

[ctb]

non-standard lineage names are not (yet) accessible from the command line; see #2469 for what I think is the latest word on them.

your best bet for now is to just put non-standard values in the standard lineage naming scheme :)

[mr-eyes]

non-standard lineage names are not (yet) accessible from the command line; see #2469 for what I think is the latest word on them.

Thank you!