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

3

Thanks for your reply.
When I re-run the phylophlan, the results give:

#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 [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist [u|k][S|G|F]GBid:taxa_level:taxonomy:avg_dist
bin.1.orig kSGB_88685:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Parapusillimonas|s__Parapusillimonas_granuli|t__SGB88685:0.01334 kSGB_88686:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae|g__Alcaligenaceae_unclassified|s__Alcaligenaceae_bacterium|t__SGB88686:0.142187
bin.15.orig uSGB_129180:Family:k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales|f__Conexibacteraceae|g__GGB44132|s__GGB44132_SGB129180|t__SGB129180:0.13776449999999998
bin.21.orig uSGB_61810:Other:k__Bacteria|p__Proteobacteria|c__CFGB14846|o__OFGB14846|f__FGB14846|g__GGB44392|s__GGB44392_SGB61810|t__SGB61810:0.15754839999999998
bin.26.strict kSGB_3343:Species:k__Bacteria|p__Planctomycetota|c__Candidatus_Brocadiia|o__Candidatus_Brocadiales|f__Candidatus_Brocadiaceae|g__Candidatus_Jettenia|s__Candidatus_Jettenia_caeni|t__SGB3343:0.0496087
bin.32.orig kSGB_3340:Species:k__Bacteria|p__Planctomycetota|c__Candidatus_Brocadiia|o__Candidatus_Brocadiales|f__Candidatus_Brocadiaceae|g__Candidatus_Kuenenia|s__Candidatus_Kuenenia_stuttgartiensis|t__SGB3340:0.011891508333333333
bin.34.strict uSGB_62879:Family:k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Aggregatilineales|f__Aggregatilineaceae|g__GGB45347|s__GGB45347_SGB62879|t__SGB62879:0.20333685714285712
bin.37.orig kSGB_89915:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Elioraeaceae|g__Elioraea|s__Elioraea_sp_Yellowstone|t__SGB89915:0.106047 kSGB_31822:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Elioraeaceae|g__Elioraea|s__Elioraea_tepidiphila|t__SGB31822:0.118728 kSGB_31823:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Elioraeaceae|g__Elioraea|s__Elioraea_thermophila|t__SGB31823:0.192258 kSGB_89913:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Elioraeaceae|g__Elioraea|s__Elioraea_rosea|t__SGB89913:0.192258 kSGB_111430:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Acetobacteraceae|g__Caldovatus|s__Caldovatus_sp_SYSU_G05006|t__SGB111430:0.196705 kSGB_89912:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Elioraeaceae|g__Elioraea|s__Elioraea_tepida|t__SGB89912:0.19673733333333332
bin.42.orig kSGB_13563:Species:k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Oceanospirillales|f__Oceanospirillaceae|g__Marinomonas|s__Marinomonas_aquimarina|t__SGB13563:0.198488 kSGB_12671:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiales_unclassified|g__Tepidimonas|s__Tepidimonas_fonticaldi|t__SGB12671:0.2388695 kSGB_61890:Species:k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas|s__Comamonas_denitrificans|t__SGB61890:0.3228138333333333
bin.44.orig kSGB_27554:Species:k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus_Nitrosocosmicus|s__Candidatus_Nitrosocosmicus_franklandus|t__SGB27554:0.0119291 kSGB_46335:Species:k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus_Nitrosocosmicus|s__Candidatus_Nitrosocosmicus_hydrocola|t__SGB46335:0.197292
bin.47.orig uSGB_62879:Family:k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Aggregatilineales|f__Aggregatilineaceae|g__GGB45347|s__GGB45347_SGB62879|t__SGB62879:0.1831687142857143
bin.6.orig kSGB_56395:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_composti|t__SGB56395:0.166649 kSGB_32198:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_sp_M4B_F_Ca_ET_013_02_1_1|t__SGB32198:0.1815416875 kSGB_11034:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_plurifarium|t__SGB11034:0.1844087142857143 kSGB_24568:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_atlanticum|t__SGB24568:0.185827 kSGB_32208:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_sp_M1D_F_Ca_ET_043_01_1_1|t__SGB32208:0.185983125 kSGB_11064:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_amorphae|t__SGB11064:0.18632900000000002 kSGB_32199:Species:k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__Bacteria_unclassified|s__bacterium_M00_F_Ca_ET_157_01_1_1|t__SGB32199:0.18724049999999995 kSGB_11037:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_sp_B2_6_2|t__SGB11037:0.18757807142857144 kSGB_11043:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_metallidurans|t__SGB11043:0.188197 kSGB_89512:Species:k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Phyllobacteriaceae|g__Mesorhizobium|s__Mesorhizobium_sp_B2_4_6|t__SGB89512:0.188685625
bin.69.strict uSGB_36412:Other:k__Bacteria|p__Chloroflexi|c__CFGB32740|o__OFGB32740|f__FGB32740|g__GGB24559|s__GGB24559_SGB36412|t__SGB36412:0.07460080000000001
bin.71.orig uSGB_62879:Family:k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Aggregatilineales|f__Aggregatilineaceae|g__GGB45347|s__GGB45347_SGB62879|t__SGB62879:0.2013227142857143
bin.12.orig is close to an SGB not present in the SGB.Jun23 database
bin.17.orig is close to an SGB not present in the SGB.Jun23 database
bin.18.orig is close to an SGB not present in the SGB.Jun23 database
bin.19.strict is close to an SGB not present in the SGB.Jun23 database
bin.2.orig is close to an SGB not present in the SGB.Jun23 database
bin.23.permissive is close to an SGB not present in the SGB.Jun23 database
bin.24.strict is close to an SGB not present in the SGB.Jun23 database
bin.3.orig is close to an SGB not present in the SGB.Jun23 database
bin.31.orig is close to an SGB not present in the SGB.Jun23 database
bin.36.strict is close to an SGB not present in the SGB.Jun23 database
bin.4.orig is close to an SGB not present in the SGB.Jun23 database
bin.40.strict is close to an SGB not present in the SGB.Jun23 database
bin.43.strict is close to an SGB not present in the SGB.Jun23 database
bin.51.orig is close to an SGB not present in the SGB.Jun23 database
bin.53.orig is close to an SGB not present in the SGB.Jun23 database
bin.56.orig is close to an SGB not present in the SGB.Jun23 database
bin.58.orig is close to an SGB not present in the SGB.Jun23 database
bin.60.orig is close to an SGB not present in the SGB.Jun23 database
bin.61.orig is close to an SGB not present in the SGB.Jun23 database
bin.63.strict is close to an SGB not present in the SGB.Jun23 database
bin.64.orig is close to an SGB not present in the SGB.Jun23 database
bin.65.orig is close to an SGB not present in the SGB.Jun23 database
bin.66.strict is close to an SGB not present in the SGB.Jun23 database
bin.67.orig is close to an SGB not present in the SGB.Jun23 database
bin.68.orig is close to an SGB not present in the SGB.Jun23 database
bin.7.orig is close to an SGB not present in the SGB.Jun23 database
bin.73.orig is close to an SGB not present in the SGB.Jun23 database
bin.74.orig is close to an SGB not present in the SGB.Jun23 database
bin.77.orig is close to an SGB not present in the SGB.Jun23 database
bin.9.orig is close to an SGB not present in the SGB.Jun23 database
bin.28.orig is close to an SGB not present in the SGB.Jun23 database
bin.38.orig is close to an SGB not present in the SGB.Jun23 database
bin.46.permissive is close to an SGB not present in the SGB.Jun23 database
bin.59.orig is close to an SGB not present in the SGB.Jun23 database
bin.30.orig is close to an SGB not present in the SGB.Jun23 database
bin.33.orig is close to an SGB not present in the SGB.Jun23 database
bin.39.orig is close to an SGB not present in the SGB.Jun23 database
bin.10.orig is not close to any SGB present in the SGB.Jun23 database
bin.11.orig is not close to any SGB present in the SGB.Jun23 database
bin.13.strict is not close to any SGB present in the SGB.Jun23 database
bin.14.orig is not close to any SGB present in the SGB.Jun23 database
bin.16.orig is not close to any SGB present in the SGB.Jun23 database
bin.20.orig is not close to any SGB present in the SGB.Jun23 database
bin.22.orig is not close to any SGB present in the SGB.Jun23 database
bin.25.orig is not close to any SGB present in the SGB.Jun23 database
bin.27.orig is not close to any SGB present in the SGB.Jun23 database
bin.29.orig is not close to any SGB present in the SGB.Jun23 database
bin.35.orig is not close to any SGB present in the SGB.Jun23 database
bin.41.strict is not close to any SGB present in the SGB.Jun23 database
bin.45.orig is not close to any SGB present in the SGB.Jun23 database
bin.48.strict is not close to any SGB present in the SGB.Jun23 database
bin.49.strict is not close to any SGB present in the SGB.Jun23 database
bin.5.orig is not close to any SGB present in the SGB.Jun23 database
bin.50.strict is not close to any SGB present in the SGB.Jun23 database
bin.52.orig is not close to any SGB present in the SGB.Jun23 database
bin.54.orig is not close to any SGB present in the SGB.Jun23 database
bin.55.strict is not close to any SGB present in the SGB.Jun23 database
bin.57.strict is not close to any SGB present in the SGB.Jun23 database
bin.62.orig is not close to any SGB present in the SGB.Jun23 database
bin.70.orig is not close to any SGB present in the SGB.Jun23 database
bin.72.orig is not close to any SGB present in the SGB.Jun23 database
bin.75.orig is not close to any SGB present in the SGB.Jun23 database
bin.76.orig is not close to any SGB present in the SGB.Jun23 database
bin.78.orig is not close to any SGB present in the SGB.Jun23 database
bin.79.orig is not close to any SGB present in the SGB.Jun23 database
bin.8.strict is not close to any SGB present in the SGB.Jun23 database

I tried with databases Jun23, Oct22 and Jan21 but the results were same.
The code is:
phylophlan_assign_sgbs -i BIN_REASSEMBLY/reassembled_bins/ -o BIN_CLASSIFICATION/phylophlan_out_Jun23 -d SGB.Jun23 --database_folder /home/hpt/PHYLOPHLAN_DATABASES -n 10 --nproc 1 --verbose 2>&1 | tee BIN_CLASSIFICATION/phylophlan_out_Jun23/phylophlan_metagenomic.log

4

Hi there and thanks for using PhyloPhlAn!

Can I ask you which metagenomic samples did you assemble? Also, did you do quality checks with CheckM on your MAGs before assigning them with PhyloPhlAn?
These are just for me to understand your situation a bit better.

Your command line looks good, and if you did the above, then the messages:

bin.12.orig is close to an SGB not present in the SGB.Jun23 database
bin.8.strict is not close to any SGB present in the SGB.Jun23 database

Should be interpreted as:

  1. […] is close […]: your MAG (bin.12.orig, for example) is close to an SGB that, however, did not meet the requirements to end up in the MetaPhlAn database, likely meaning is an SGB with too few MAGs (in that specific database version, Jun23 in your case).
  2. […] is not close […]: your MAG (bin.8.strict, for example) is not close to the SGBs as in that database (Jun23 in your case), so can likely define a new SGB cluster if added to our SGB resource.

I hope this can help! And please let me know about my questions above, which can help us understand your situation better.

Many thanks,
Francesco