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taxonomy_recovery [2020/10/26 10:15] – 24.138.68.92taxonomy_recovery [2024/06/11 10:31] (current) – 129.173.94.151
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    acc2tax -i /db1/extra-data-sets/Acc2tax/acc2taxIN_example -p -d /db1/extra-data-sets/Acc2tax/Acc2Tax_071119 -o taxonomy.out    acc2tax -i /db1/extra-data-sets/Acc2tax/acc2taxIN_example -p -d /db1/extra-data-sets/Acc2tax/Acc2Tax_071119 -o taxonomy.out
  
-don't forget to make sure that your input file contains only the accession numbers without their version, see the example file given above.+don't forget to make sure that your input file contains only the accession numbers without their version, see the example file given above.  
 + 
 +:-( E.g., MBI4782295.1 shall be MBI4782295, otherwise the bugs will occur: 
 + 
 +<code> 
 +Couldn't find: [MBI4782295.1] 
 + 
 +</code> 
 + 
 +:-D Trim the version ".1" behind the accession MBI4782295.1 
 + 
 +<code> 
 +> cat file | cut -d '.' -f1 > out_file 
 + 
 +</code> 
 + 
 +Note:  
 +1. You can get the accession list from Blast/Plast result (output.txt) directly using the command below: 
 + 
 +<code> 
 +> cat output.txt | cut  -f2 | cut -d '.' -f1 > out_file 
 +</code> 
 + 
 +2. If there are "|" in the accession numbers (i.e., gb|KAA8922376.1|) 
 + 
 +<code> 
 +> cat output.txt | cut -d "|" -f2 | cut -d '.' -f1 > out_file 
 +</code> 
 + 
 +3. It can still acquire a list of unknown like below even the NCBI taxonomy database is updated to the latest. 
 + 
 +<code> 
 +Couldn't find: [MBR3349819] 
 +Couldn't find: [HBS54143] 
 +Couldn't find: [MYJ28876] 
 +</code> 
 + 
 +This might due to these protein IDs(MBR3349819,HBS54143) from the species cannot put into the taxonomy like NP_051083. i.e., Lineage is not in (full) status. 
 + 
 + 
 +<code> 
 +NP_051083 cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliopsida,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Brassicales,Brassicaceae,Camelineae,Arabidopsis,Arabidopsis thaliana 
 +</code>
  
 ========================== ==========================
-acc2tax database:\\+acc2tax database Location:\\ 
 + 
 +/db1/extra-data-sets/Acc2tax/ 
 + 
 +/db1/extra-data-sets/Acc2tax/Acc2Tax_04_01_2024 (Up to date Jan 04, 2024) 
 + 
 +\\
  
-/scratch3/rogerlab_databases/other_dbs/acc2tax_Sept2020 (Up to date Sept 28, 2020)\\+<Last updated by Dandan Zhao on Jun 11, 2024>
taxonomy_recovery.1603718135.txt.gz · Last modified: by 24.138.68.92