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usearch9 not found when generate UTAX database #104

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tangyuhua36 opened this issue Dec 4, 2023 · 0 comments
Open

usearch9 not found when generate UTAX database #104

tangyuhua36 opened this issue Dec 4, 2023 · 0 comments

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@tangyuhua36
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When I tried to build custom COI database,I got this error in step #generate UTAX database
##########this is my code
amptk database -i arth10000.BIN-consensus.fasta -f LCO1490 -r GGWACTAATCAATTTCCAAATCC --primer_required rev \

--derep_fulllength --format off --subsample 00000 --primer_mismatch 4 -o COI02_UTAX --min_len 200 \
--create_db utax --install --source NCBI

[05:14:28 PM]: OS: Ubuntu 20.04, 8 cores, ~ 17 GB RAM. Python: 3.10.13
[05:14:28 PM]: AMPtk v1.6.0, VSEARCH v2.25.0
[05:14:28 PM]: Base name set to: /home/tanyihua/miniconda3/envs/amptk/lib/python3.10/site-packages/amptk/DB/COI02_UTAX
[05:14:28 PM]: Searching for primers, this may take awhile: Fwd: GGTCAACAAATCATAAAGATATTGG Rev: GGATTTGGAAATTGATTAGTWCC
[05:14:28 PM]: 6,067 records loaded
[05:14:28 PM]: Using 8 cpus to process data
[05:14:29 PM]: 1 records passed (0.02%)
[05:14:29 PM]: Errors: 0 no taxonomy info, 0 no ID, 5,777 length out of range, 0 too many ambiguous bases, 289 no primers found
[05:14:29 PM]: Now dereplicating sequences (collapsing identical sequences)
[05:14:29 PM]: 1 records passed (0.02%)
[05:14:29 PM]: Creating UTAX Database, this may take awhile
Traceback (most recent call last):
File "/home/tanyihua/miniconda3/envs/amptk/bin/amptk", line 10, in
sys.exit(main())
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/site-packages/amptk/amptk.py", line 784, in main
mod.main(arguments)
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/site-packages/amptk/extract_region.py", line 673, in main
makeDB(OutName, args=args)
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/site-packages/amptk/extract_region.py", line 419, in makeDB
subprocess.call([usearch, '-makeudb_utax', input,
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/subprocess.py", line 345, in call
with Popen(*popenargs, **kwargs) as p:
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/subprocess.py", line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/tanyihua/miniconda3/envs/amptk/lib/python3.10/subprocess.py", line 1863, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'usearch9'
##########
Why this happened?

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