notes.txt

accession_taxid  names            nodes          
sqlite> select * from names LIMIT 10;
taxid|name
1|root
2|Bacteria <bacteria>
6|Azorhizobium
7|Azorhizobium caulinodans
9|Buchnera aphidicola
10|Cellvibrio
11|Cellulomonas gilvus
13|Dictyoglomus
14|Dictyoglomus thermophilum
16|Methylophilus

sqlite> select * from nodes LIMIT 10;
taxid|parent_taxid|rank
1|1|-
2|131567|superkingdom
6|335928|genus
7|6|species
9|32199|species
10|1706371|genus
11|1707|species
13|203488|genus
14|13|species
16|32011|genus

sqlite> select * from accession_taxid LIMIT 10;
accession|taxid
A00001.1|10641
A00002.1|9913
A00003.1|9913
A00004.1|32630
A00005.1|32630
A00006.1|32630
A00008.1|32630
A00009.1|32630
A00010.1|32630
A00011.1|32630

A.taxId NCBI_node
B.nameTxt NCBI_name
WHERE
A.taxId = B.taxId
AND NCBI_node.parentTaxId = taxid


6965 ../output_data/child_test.csv

wc -l blacklist_2
	7346421


10:41 hadley_king@hive1-node1 ~ $ nohup python3 git_filtered_nt/ac2taxid_check.py -d ncbi-taxonomy-database/taxonomy.db -n raw_data/nt -l logs/logfile.accession2taxid.txt & 
ps ax | grep 'ac2taxid_check.py'

accession|taxid|name|parent_taxid|rank

https://ncbi-hackathons.github.io/EDirectCookbook/

cat logs/logfile.accession2taxid_test.txt | epost -db nuccore -format acc | elink -target taxonomy | efetch -format xml | xtract -pattern Taxon -element TaxId, ScientificName, Rank, Lineage




#______________________________________________________________________________#
   Monday    06-26-23
   
   1,512,606
   1,576,990
   
   656650780
   656981344
   
   make nucleotide
330564 /tmp/tmp.UqzDSlVl2g
656981344 /tmp/tmp.UqzDSlVl2g
972514815 /tmp/tmp.UqzDSlVl2g


330564 /tmp/tmp.YJcTZpo3kb
656981344 /tmp/tmp.YJcTZpo3kb
972,514,815 /tmp/tmp.YJcTZpo3kb
972,514,757 /tmp/tmp.kb7bmdsyZl

PID: 2784320

14,384,694,720 * 0.06 = 863,081,683.2

36,331,904

93,245,213 nt

11,283,515