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

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”