No metabat_bin is assigned by PhyloPhlan --- metabat_bin.# is close to an SGB not present in the SGB.Jun23 database

Microbial community profiling PhyloPhlAn
1

Hello, Thank you for the tool.
However, I cannot get any species assignment when I run phylophlan_assign_sgbs.
This is the result for phylophlan_out.tsv
#input_bin [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist
metabat_bin.6 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.53 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.26 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.51 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.62 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.65 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.82 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.27 is close to an SGB not present in the SGB.Jun23 database
metabat_bin.14 is close to an SGB not present in the SGB.Jun23 database
…

And this is the command run line:
(base) hpt@DESKTOP-1SR3IAI:~/MAG_run$ phylophlan_assign_sgbs -i metabat2/metabat2_bins/ -o metabat2/phylophlan_out -d SGB.Jun23 --nproc 10 --verbose 2>&1|tee metabat2/phylophlan_out/phylophlan_metagenomic.log
phylophlan_assign_sgbs.py version 3.1.40 (6 March 2024)

Command line: /home/hpt/anaconda3/bin/phylophlan_assign_sgbs -i metabat2/metabat2_bins/ -o metabat2/phylophlan_out -d SGB.Jun23 --nproc 10 --verbose

Setting input extension to “.fa”
Output prefix is a folder, setting it to “metabat2/phylophlan_out/phylophlan_out”
Creating folder “metabat2/phylophlan_out/phylophlan_out_sketches”
Creating folder “metabat2/phylophlan_out/phylophlan_out_sketches/inputs”
Creating folder “metabat2/phylophlan_out/phylophlan_out_dists”
Creating folder “metabat2/phylophlan_out/phylophlan_out_prefiltering”
Creating folder “metabat2/phylophlan_out/phylophlan_out_prefiltering/pref_dbs”

Arguments: {‘input’: ‘metabat2/metabat2_bins/’, ‘output_prefix’: ‘metabat2/phylophlan_out/phylophlan_out’, ‘database’: ‘SGB.Jun23’, ‘database_list’: False, ‘database_update’: False, ‘input_extension’: ‘.fa’, ‘how_many’: 8, ‘nproc’: 10, ‘database_folder’: ‘phylophlan_databases/’, ‘only_input’: False, ‘add_ggb_fgb’: False, ‘overwrite’: False, ‘verbose’: True, ‘mapping’: ‘SGB.Jun23.txt.bz2’}

Checking “mash”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/87813_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/51063.bz2_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/64990.bz2_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/37198.bz2_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/33811_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/2626_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/8227_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/93267.bz2_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/15647_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/40144_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/10607.bz2_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/7135_paste.msh”
Pasting “metabat2/phylophlan_out/phylophlan_out_prefiltering/13060.bz2_paste.msh”
Inputs pasted in 77s
Disting “phylophlan_databases/SGB.Jun23/27659.msh”
Disting “phylophlan_databases/SGB.Jun23/111467.msh”
Disting “phylophlan_databases/SGB.Jun23/25589.msh”
Disting “phylophlan_databases/SGB.Jun23/111540.msh”
Disting “phylophlan_databases/SGB.Jun23/19010.msh”
Disting “phylophlan_databases/SGB.Jun23/14333.bz2.msh”
Disting “phylophlan_databases/SGB.Jun23/38743.bz2.msh”
Disting “phylophlan_databases/SGB.Jun23/45790.msh”
Disting “phylophlan_databases/SGB.Jun23/9774.bz2.msh”
Disting “phylophlan_databases/SGB.Jun23/12780.msh”
Removing “metabat2/phylophlan_out/phylophlan_out_dists/14333.bz2.tsv”

Removing “metabat2/phylophlan_out/phylophlan_out_dists/38743.bz2.tsv”
[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/14333.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/14333.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] cannot execute command
mash dist -p 1 phylophlan_databases/SGB.Jun23/14333.bz2.msh metabat2/phylophlan_out/phylophlan_out_prefiltering/14333.bz2_paste.msh
Dist for “phylophlan_databases/SGB.Jun23/111540.msh” computed in 0s

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/14333.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/14333.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/38743.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/38743.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] error while disting
metabat2/phylophlan_out/phylophlan_out_prefiltering/14333.bz2_paste.msh
phylophlan_databases/SGB.Jun23/{}.msh
metabat2/phylophlan_out/phylophlan_out_dists/14333.bz2.tsv
True

[e] cannot execute command
mash dist -p 1 phylophlan_databases/SGB.Jun23/38743.bz2.msh metabat2/phylophlan_out/phylophlan_out_prefiltering/38743.bz2_paste.msh

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/38743.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/38743.bz2_paste.msh’]’ returned non-zero exit status 1.
Dist for “phylophlan_databases/SGB.Jun23/27659.msh” computed in 0s

[e] error while disting
metabat2/phylophlan_out/phylophlan_out_prefiltering/38743.bz2_paste.msh
phylophlan_databases/SGB.Jun23/{}.msh
metabat2/phylophlan_out/phylophlan_out_dists/38743.bz2.tsv
True
Dist for “phylophlan_databases/SGB.Jun23/111467.msh” computed in 0s
Dist for “phylophlan_databases/SGB.Jun23/12780.msh” computed in 0s
Removing “metabat2/phylophlan_out/phylophlan_out_dists/9774.bz2.tsv”
Dist for “phylophlan_databases/SGB.Jun23/25589.msh” computed in 0s

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/9774.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/9774.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] cannot execute command
mash dist -p 1 phylophlan_databases/SGB.Jun23/9774.bz2.msh metabat2/phylophlan_out/phylophlan_out_prefiltering/9774.bz2_paste.msh

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/9774.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/9774.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] error while disting
metabat2/phylophlan_out/phylophlan_out_prefiltering/9774.bz2_paste.msh
phylophlan_databases/SGB.Jun23/{}.msh
metabat2/phylophlan_out/phylophlan_out_dists/9774.bz2.tsv
True
Dist for “phylophlan_databases/SGB.Jun23/19010.msh” computed in 0s
Dist for “phylophlan_databases/SGB.Jun23/45790.msh” computed in 0s

[e] Command ‘[‘mash’, ‘dist’, ‘-p’, ‘1’, ‘phylophlan_databases/SGB.Jun23/38743.bz2.msh’, ‘metabat2/phylophlan_out/phylophlan_out_prefiltering/38743.bz2_paste.msh’]’ returned non-zero exit status 1.

[e] disting crashed
Loading SGB mapping file
Loading mash dist files
Removing “unassigned.txt”
Results saved to “metabat2/phylophlan_out/phylophlan_out.tsv”

2

Hello there,

the message

metabat_bin.26 is close to an SGB not present in the SGB.Jun23 database

is provided when the input MAG is not similar enough to the public set of SGBs we distribute. So, in that case, we have a very small SGB cluster in our full database, but it is not large enough to be considered by MetaPhlAn in the analysis and, hence, be publicly available.

However, your other output log seems to have an error with Mash. Have you tried cleaning up the temporary files and checking if the error persists?

Thanks,
Francesco