Update to motus 3

tax_practical/README.md

@@ -245,24 +245,24 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
    You can profile the sample with:
    
    ```
-   motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus
+   motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 8
    ```
    
    Which produces (`head test_sample.motus`):
    ```
-   # git tag version 2.5.1 |  motus version 2.5.1 | map_tax 2.5.1 | gene database: nr2.5.1 | calc_mgc 2.5.1 -y insert.scaled_counts -l 75 | calc_motu 2.5.1 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_2.5.1 meta_mOTU_2.5.1
-   # call: python motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus
-   #consensus_taxonomy	unnamed sample
-   Leptospira alexanderi [ref_mOTU_v25_00001]	0.0000000000
-   Leptospira weilii [ref_mOTU_v25_00002]	0.0000000000
-   Chryseobacterium sp. [ref_mOTU_v25_00004]	0.0000000000
-   Chryseobacterium gallinarum [ref_mOTU_v25_00005]	0.0000000000
-   Chryseobacterium indologenes [ref_mOTU_v25_00006]	0.0000000000
-   Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v25_00007]	0.0000000000
-   Chryseobacterium jejuense [ref_mOTU_v25_00008]	0.0000000000
-   ```
-   In the profile, `ref_mOTU` represent species with a reference genome sequence in NCBI. While `meta_mOTU` represent species that have not been sequenced yet (they do not have a representative genome in NCBI).
-   the `-1` at the end of the file (check with `tail test_sample.motus`), represents species that we know to be present, but are not able to profile. The `-1` is useful to have a correct evaluation of the relative abundance of all species (more info [here](https://github.com/motu-tool/mOTUs_v2/wiki/Explain-the-resulting-profile#-1)).
+# git tag version 3.0.0 |  motus version 3.0.0 | map_tax 3.0.0 | gene database: nr3.0.0 | calc_mgc 3.0.0 -y insert.scaled_counts -l 75 | calc_motu 3.0.0 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_3.0.0 meta_mOTU_3.0.0
+# call: python /g/scb2/zeller/milanese/motus_v2/update_DB/mOTUs/motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 16
+#consensus_taxonomy	unnamed sample
+Leptospira alexanderi [ref_mOTU_v3_00001]	0.0000000000
+Leptospira weilii [ref_mOTU_v3_00002]	0.0000000000
+Chryseobacterium sp. [ref_mOTU_v3_00004]	0.0000000000
+Chryseobacterium gallinarum [ref_mOTU_v3_00005]	0.0000000000
+Chryseobacterium indologenes [ref_mOTU_v3_00006]	0.0000000000
+Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v3_00007]	0.0000000000
+Chryseobacterium jejuense [ref_mOTU_v3_00008]	0.0000000000
+   ```
+   In the profile, `ref_mOTU` represent species with a reference genome sequence in NCBI. While `meta_mOTU` and `ext_mOTU` represent species that have not been sequenced yet (they do not have a representative genome in NCBI).
+   the `unassigned` at the end of the file (check with `tail test_sample.motus`), represents species that we know to be present, but are not able to profile. The `unassigned` is useful to have a correct evaluation of the relative abundance of all species (more info [here](https://github.com/motu-tool/mOTUs_v2/wiki/Explain-the-resulting-profile#-1)).
    </p> 
 
 2. How many species are detected? How many are reference species and how many are unknown species?