Error while writing fasta files

[yurunxian]

Hi!
I encountered a error when execuated avp prepare. When the avp prepare finished extracting hits from DB, an error showed up.
The seq name in ./tmp/setblast.fa looks like ">KAG6554565.1@56867", so I thought I correctely prepared the NR database. I also found although there are 151483 seq names in ./tmp/extract_id.txt, a total of 226185 seqs are present in ./tmp/setblast.fa.

[+] Setting up
[!] Selected 3156 HGT candidates
[+] Parsing hits file and grouping similar queries
[!] Formed 2814 groups
[+] Extracting hits from DB
[+] Writing fasta files
Traceback (most recent call last):
File "/data/yurx/software/AvP/avp", line 7, in
main()
File "/data/yurx/software/AvP/depot/interface.py", line 29, in main
prepare.main()
File "/data/yurx/software/AvP/depot/prepare.py", line 333, in main
lname = ncbi.translate_to_names(lnode) # This does not output them in order
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/yurx/anaconda3/envs/AvP/lib/python3.12/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 324, in translate_to_names
id2name = self.get_taxid_translator(taxids)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/yurx/anaconda3/envs/AvP/lib/python3.12/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 268, in get_taxid_translator
result = self.db.execute(cmd)
^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: no such column: "1" - should this be a string literal in single-quotes?<

As I have several species to analyze, the error message varies among different analyses. For example, in another species:

sqlite3.OperationalError: no such column: "574976" - should this be a string literal in single-quotes?

Could you please help check out this issue? Thanks!

[GDKO]

Hi @yurunxian ,

Did you run diamond or blast with NR?

[yurunxian]

Thanks for your reply!@GDKO I run diamond v2.1.11.165 with NR according to #[11]. It yeilded a 300Mb output file with standart outfmt6 and taxids.

[GDKO]

Can you post your config file?

[yurunxian]

---

max_threads: 16

DB path

blast_db_path: /data/public_data_repository/NR/nr # blast: change to the local blast_db path
fasta_path: # diamond: change to the local fasta path for sp, ur90, or custom database
mode: blast # use blast for blast database, use sp for swissprot database, ur90 for uniref90 or custom database
data_type: AA # data type DNA, AA

Algorithm options

prepare

ai_cutoff: 0
ahs_cutoff: 0
outg_pct_cutoff: 80
selection: "ai or ahs" # select sequences based on which metrics, another example "(ai or ahs) and outg_pct"
percent_identity: 100 # select hits equal or below this number
cutoffextend: 20 # when ingroup hit is found, we take this hit + n hits
number_hits_noingroup: 50 # when no ingroup hit is found, we take this number of hits
trimal: false
min_num_hits: 4 # select queries with at least that many blast hits
percentage_similar_hits: 0.7 # group queries based on this

detect, clasify, evaluate

fastml: true # Use fasttree instead of IQTree
node_support: 0 # nodes below that number will collapse
complex_per_ingroup: 20 # if D/(D+I) smaller than this then node is considered Ingroup
complex_per_donor: 80 # if D/(D+I) greater than this then node is considered Donor
complex_per_node: 90 # if node contains percent number of this category, it is assigned

Program specific options

mafft_options: '--anysymbol --auto'
trimal_options: '-automated1'

#IQ-Tree
iqmodel: '-mset WAG,LG,JTT -AICc -mrate E,I,G,R'
ufbootstrap: 1000
iq_threads: 4

[GDKO]

The config file looks good.

Can you maybe send me the avp output folder together with the files you used with avp prepare to my personal email?

[yurunxian]

Hi @GDKO , I finally solved this issue. It was due to a small bug in ete3 package, so I replaced the ete3 with ete4 in the line 28 of prepare.py. Please find the details in the link below.
from ete4 import NCBITaxa

https://github.com/etetoolkit/ete/pull/770