Missing Assigned Taxon IDs

[ardasevkar]

I was reviewing the MaltExtract outputs and noticed that results for specific organisms (listed below) are missing:

• Achromobacter denitrificans
• Bacteroides vulgatus
• Citrobacter koseri
• Enterococcus hirae
• Fusobacterium necrophorum
• Haemophilus parainfluenzae
• Leuconostoc mesenteroides
• Providencia heimbachae
• Rickettsia raoultii
• Staphylococcus cohnii
• Staphylococcus saprophyticus
• Streptococcus intermedius
• Streptococcus pyogenes

I've checked the log file of MaltExtract, and I found an error message stating: <Species_name> has no assigned taxID and cannot be processed! Consider checking for a error in filepath if you provided a taxon file as input

I'm using the NCBI.tre files that come with HOPS, which are located under the Resources folder. If you need it, you can find my code to run MaltExtract below:

java -Xmx500G -jar /usr/local/sw/anaconda3/envs/aMeta/share/hops-0.35-1/MaltExtract1.7.jar -i results/MALT/${lib_id}.rma6 -f def_anc -o results/MALT_EXTRACT --reads --destackingOff --downSampOff --dupRemOff --threads 20 --resources ~/programs/HOPS/Resources --matches --minPI 85.0 --maxReadLength 0 --minComp 0.0 --meganSummary -t results/MALT_EXTRACT/taxa