(doc inconsistency) Convert annotation to RowDiff<Multi-BRWT>

[shenwei356]

Hi, I'm playing with metagraph, while I found the doc might not be updated with the lastest metagraph version.

On my laptop, I tried to install via conda, but it failed due to htslib and libdeflate version conflict. (**11 July update: I succeed to install in the server**)

The following packages are incompatible
└─ metagraph 0.3.6  is not installable because there are no viable options
   ├─ metagraph 0.3.6 would require
   │  └─ htslib [>=1.16,<1.21.0a0 |>=1.17,<1.21.0a0 ] but there are no viable options
   │     ├─ htslib 1.20 would require
   │     │  └─ libdeflate >=1.20,<1.21.0a0 , which conflicts with any installable versions previously reported;
   │     ├─ htslib [1.17|1.18|1.19|1.19.1|1.20] would require
   │     │  └─ libdeflate >=1.18,<1.21.0a0 , which conflicts with any installable versions previously reported;
   │     └─ htslib [1.15.1|1.16|1.17] would require
   │        └─ libdeflate >=1.13,<1.21.0a0 , which conflicts with any installable versions previously reported;
   ├─ metagraph 0.3.6 would require
   │  └─ htslib >=1.15.1,<1.21.0a0  but there are no viable options
   │     ├─ htslib 1.20, which cannot be installed (as previously explained);
   │     ├─ htslib [1.17|1.18|1.19|1.19.1|1.20], which cannot be installed (as previously explained);
   │     ├─ htslib [1.15.1|1.16|1.17], which cannot be installed (as previously explained);
   │     └─ htslib 1.15.1 would require
   │        └─ libdeflate >=1.10,<1.21.0a0 , which conflicts with any installable versions previously reported;
   └─ metagraph 0.3.6 would require
      └─ htslib >=1.20,<1.21.0a0 , which cannot be installed (as previously explained)

So I installed it via docker, which is easy to install but not easy to use.

$ sudo docker pull ghcr.io/ratschlab/metagraph:master
master: Pulling from ratschlab/metagraph
560c024910be: Pull complete 
73741faf56e2: Pull complete 
9fef9ccec059: Pull complete 
9f7e509ed7b4: Pull complete 
f130c8f6aa01: Pull complete 
d6c08dbd5c81: Pull complete 
f75225651ddd: Pull complete 
6e8f1b987c4c: Pull complete 
Digest: sha256:e75184a4e4defc98466fd1c720261bd08c172f854ed27841b87b83e572279d6a
Status: Downloaded newer image for ghcr.io/ratschlab/metagraph:master
ghcr.io/ratschlab/metagraph:master

Here's the step of indexing, the input is 200 bacterial assemblies. Everything is OK, and I can align the index. BTW, I ran the alignment function with a 16S rRNA gene, it only returned one alignment even if setting it to return 1000 alignments, which is far less than expected.

## Index

    # Build the graph
    ls test200_/* \
        | sed 's/^/\/mnt\//' \
        | sudo docker run -i -v .:/mnt ghcr.io/ratschlab/metagraph:master build -v -p 16 -k 31 -o /mnt/graph


    # Index k-mer coordinates
    ls test200_/* \
        | sed 's/^/\/mnt\//' \
        | sudo docker run -i -v .:/mnt ghcr.io/ratschlab/metagraph:master \
            annotate -v -p 16 -i /mnt/graph.dbg --anno-filename --coordinates  -o /mnt/annotation

## align

    sudo docker run -i -v .:/mnt ghcr.io/ratschlab/metagraph:master \
        align -v -p 16 -i /mnt/graph.dbg -a /mnt/annotation.row.annodbg \
            --align-alternative-alignments 1000 \
            --align-min-seed-length 15 \
            /mnt/t.16S.fa > metagraph.txt

And I would like to query with coordinates, following the steps here: Convert annotation to RowDiff. The guide does not specify the output base, and metagraph reported usage error.

metagraph: /lib/x86_64-linux-gnu/libhts.so.3: no version information available (required by metagraph)
Usage: metagraph transform_anno -o <annotation-basename> [options] ANNOTATOR

So I added -o, and the 3 stages worked well.

    for s in 0 1 2; do
        find . -name "*.column.annodbg" \
            | sed 's/^/\/mnt\//' \
            | sudo docker run -i -v .:/mnt ghcr.io/ratschlab/metagraph:master \
                transform_anno -v -p 16 --anno-type row_diff --coordinates --row-diff-stage $s \
                    -o /mnt/annotation -i /mnt/graph.dbg
    done

But for the next step, which needs the input of *.row_diff.annodbg, I can't find them.

find . -name "*.row_diff.annodbg" | ...

Files:

annotation.column.annodbg         annotation.row_reduction  graph.dbg.anchors        graph.dbg.succ           t.16S.fa
annotation.column.annodbg.coords  db.lmi                    graph.dbg.pred           graph.dbg.succ_boundary  test200_
annotation.row.annodbg            doc.md                    graph.dbg.pred_boundary  xxx.txt
annotation.row_count              graph.dbg                 graph.dbg.rd_succ        metagraph.txt

So I guess the doc might need to be updated.