did not find a decorated file for the archaeal tree

[Yi Liu]

Hi Simon,

Thanks for your useful tool!

but i met a issue when i added the test MAGs to database. I first ran the wetland MAGs test and was able to get the correct output, but when adding my custom MAG database it was unable to recognize my decorated.tree-taxonomy files even though they existed.

I am using gtdbtk: version 1.5.0:

emma@emma-PowerEdge-R730xd:/media/HD1/LY/MAGs_GTDB-tk_results$ ll
total 10076
-rw-rw-r-- 1 emma emma 145267 8月 28 15:28 gtdbtk.ar122.decorated.tree
-rw-rw-r-- 1 emma emma 391682 9月 1 21:58 gtdbtk.ar122.decorated.tree-taxonomy
-rw-rw-r-- 1 emma emma 2538861 8月 28 15:28 gtdbtk.bac120.decorated.tree
-rw-rw-r-- 1 emma emma 7231288 9月 1 21:58 gtdbtk.bac120.decorated.tree-taxonomy
drwxrwxr-x 2 emma emma 4096 9月 2 17:07 infer

emma@emma-PowerEdge-R730xd:/media/HD1/LY/MAGs_GTDB-tk_results$ cd ./infer
emma@emma-PowerEdge-R730xd:/media/HD1/LY/MAGs_GTDB-tk_results/infer$ ll
total 2624
-rw-rw-r-- 1 emma emma 145267 9月 1 21:58 gtdbtk.ar122.decorated.tree
-rw-rw-r-- 1 emma emma 2538861 9月 1 21:58 gtdbtk.bac120.decorated.tree

my command:

nohup iphop add_to_db --fna_dir /media/HD1/LY/dereplicated_genomes --gtdb_dir /media/HD1/LY/MAGs_GTDB-tk_results --out_dir /media/HD1/LY/host_predictions/iphop_db_with_custom_mags --db_dir /media/HD1/LY/Aug_2023_pub_rw --num_threads 32 &

head of the logfile:

Starting
[1] Get a list of genomes to import...
[2] Import information from GTDBtk trees...
Reading /media/HD1/LY/MAGs_GTDB-tk_results/gtdbtk.ar122.decorated.tree
Reading /media/HD1/LY/MAGs_GTDB-tk_results/gtdbtk.bac120.decorated.tree
[3] Load new host genomes in blast database...

Building a new DB, current time: 09/02/2024 17:13:30
New DB name: /media/HD1/LY/host_predictions/iphop_db_with_custom_mags/db/Host_Genomes/New_host_genomes
New DB title: /media/HD1/LY/host_predictions/iphop_db_with_custom_mags/db/Host_Genomes/New_host_genomes.fna
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 2255758 sequences in 171.545 seconds.

Created nucleotide BLAST (alias) database /media/HD1/LY/host_predictions/iphop_db_with_custom_mags/db/Host_Genomes/Host_Genomes with 25402714 sequences
[4] Get CRISPR arrays from new MAGs and add to database...
python /home/emma/mambaforge/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/CRISPR/identify_crispr.folder.py -i /media/HD1/LY/dereplicated_genomes -o /media/HD1/LY/host_predictions/iphop_db_with_custom_mags/db/Tmp_CRISPRs
python /home/emma/mambaforge/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/CRISPR/get_crispr_database.py -d /media/HD1/LY/host_predictions/iphop_db_with_custom_mags/db/Tmp_CRISPRs
[5] Add new genomes to WIsH database...

[6] Add new genomes to VHM database...
[7] Add new genomes to PHP database...
counting kmer ...
Processing adh_s_bin463.fna
Processing dbc_w_bin326.fna
Processing blk_s_bin263.fna

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tail of the logfile:

Note: xcd_s_bin691 will not be included in the database because it could not be added to any tree (bacteria or archaea)
Note: gskl_s_bin495 will not be included in the database because it could not be added to any tree (bacteria or archaea)
Note: dbc_s_bin326 will not be included in the database because it could not be added to any tree (bacteria or archaea)
Note: dbc_w_bin82 will not be included in the database because it could not be added to any tree (bacteria or archaea)

We added 0 additional bacteria genomes and 0 additional archaea genomes
[9] All done

!#!#!#!#!#! WARNING --- SOME UNEXPECTED EVENTS HAPPENED -- WE LIST THEM BELOW, IT COULD BE NOTHING, BUT YOU SHOULD STILL DOUBLE-CHECK #!#!#!#!#!#!#

Note - we did not find a decorated file for the archaeal tree, so we did not use any data from a new archaeal genome
Note - we did not find a decorated file for the bacterial tree, so we did not use any data from a new bacterial genome

!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!!#!#!#!#!#!#!

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[Simon Roux]

Hi,
So it seems like iPHoP does find the tree files, but can not identify the bins in these trees. Can you check if the bins (e.g. dbc_w_bin82) are indeed mentioned in these files, and if they have the exact same name ?

[Yi Liu]

Thank you for your quick response. I checked the tree files. The bins are indeed mentioned in these files, and they have exact same name.

dbc_w_bin500 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__; s__

GB_GCA_002453155.1 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__UBA6776; s__UBA6776 sp002453155
gskl_w_bin81 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__; s__
GB_GCA_013216195.1 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__JABSOQ01; s__JABSOQ01 sp013216195
xcd_s_bin612 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__; s__
dbc_w_bin520 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__; s__
dbc_w_bin82 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__; s__
GB_GCA_001769925.1 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__RBG-16-40-8; s__RBG-16-40-8 sp001769925
GB_GCA_903833275.1 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__RBG-16-40-8; s__RBG-16-40-8 sp903833275
GB_GCA_003694355.1 d__Bacteria; p__Bdellovibrionota; c__Bdellovibrionia; o__Bdellovibrionales; f__UBA1609; g__J124; s__J124 sp003694355

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[Simon Roux]

Ok, I think I see what happens. GTDB-tk changed where some files are stored between versions, so iPHoP is confused. Can you try to copy the files “gtdbtk.ar122.decorated.tree-taxonomy” and “gtdbtk.bac120.decorated.tree-taxonomy” from “MAGs_GTDB-tk_results/” to “MAGs_GTDB-tk_results/infer/” ? iPHoP expects these two to be in “infer/”, but with 1.5 it seems they are only in the base directory, and infer only contains the “decorated.tree” files. Then delete the custom database directory you already generated, re-run “add_to_db”, and hopefully you won’t see these warnings anymore, and you will see your MAGs in the “Host_Genomes.tsv” file

[Yi Liu]

Hi Simon,

It works. Thank you so much!

[8] Now build the new host genome metadata file...

We added 4271 additional bacteria genomes and 465 additional archaea genomes
[9] All done

[Simon Roux]

Great, thanks for the follow up !

[Simon Roux]

Problem fixed