Dear developers,
I met a problem when running strainphlan(under metaphlan version=4.2.4) with command ”sample2markers.py -i vdb3.sam -f sam -o consensus_markers2 -n 1 -d /mpa_vOct22_CHOCOPhlAnSGB_202403.pkl”.It shows:[E::sam_hrecs_refs_from_targets_array] Duplicate entry “VDB|003B_0000_0_01C2|M1_c0_c0_c0” in target list
[E::sam_parse1] failed to parse header
I wonder if sample2markers.py cannot identification the information which in the SAM file that start with “VDB“.Because I reviewed the script and found that lines 58-59 showed “if marker.startwih(“VDB”): return Fasle“, and in another test I conducted, after deleting all the information strating with “VDB“ in the SAM file, the script could run normally
