Samples2markers.py: MarkerXX not in the metaphlan database

Microbial community profiling StrainPhlAn
1

I have met the a problem, and my steps are same as the tutorial in git hub.

> Marker UniRef90_A0A1N4W9S2|5__8|SGB16955 not in the metaphlan database

My sam files look like

> FP180000019BRL1C015R02000021589/1__1.92 16 UniRef90_A0A2W5IBW0|1__6|SGB3663 280 42 150M * 0 0 CCCGAGTGGATACAACCTGACGCCGCAGACAATATATACGCATTTGCACAGGGGCCATCTGGCGCTTTCGCAGGTTTTGCACATTGGCATCACGGTAAATTAGAACGTGCTTTCACCGCGACAACCTGCGAAATTCTGGAGGATAAAGGG FFFFFFFF888F88,FF8F,8F88F888FF8F888FFF8FFFFFF88F8FFFFFF8FF8F8F8FFFFF8F8FFFFFFFFFFFFF8FFFFF8F8FFF8F8F888FF8FFFFFFF8FF8FFFF8FFFFFFF8F8FFFFFFF8FFF8888FFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150 YT:Z:UU

they have the same format with the id in “mpa_vOct22_CHOCOPhlAnSGB_202403_marker_info.txt” file ,and I’m sure use mpa_vOct22_CHOCOPhlAnSGB_202403 version of database for both metaphlan and samples2markers.py. How can I fix it?
can anyone help me ?

2

my commands

> 
> metaphlan ${inputdir}/${k}_repaired_1.fastq,${inputdir}/${k}_repaired_2.fastq --nproc 20 --index mpa_vOct22_CHOCOPhlAnSGB_202403 --input_type fastq -s ${sams}/${k}.sam.bz2 --bowtie2out ${bowtie2}/${k}.bowtie2.bz2 -o ${profiles}/${k}_profiled.tsv
> 
> sample2markers.py -i ${sams}/${k}.sam.bz2 -o ${consensus_markers} -n 20 -d ${db}
3

Hi @Joe

I had a look and the marker UniRef90_A0A1N4W9S2|5__8|SGB16955 is not present in the Oct22 database, but in the Jun23 database. Are you sure you ran metaphlan with the Oct22? You can check the SAM file with grep for @PG header to see the command line the bowtie2 was ran with and the parameter -x there to see which database it used.
Best regards

Michal