Hello, when I try to build a database with accessions file, I met the error like this:
haystac database --mode build --output pathogen --accessions-file pathogenlist1.txt
usage: haystac database --mode --output [--query ]
[--query-file ] [--accessions-file ]
[--sequences-file ] [--refseq-rep
Even the basic example command cannot run correctly.
$ haystac database --mode build --query '"Yersinia"[Organism] AND "complete genome"[All field]' --output yersinia_example
HAYSTAC v 0.4.10
Date: 2024-03-05 17:59:06.818678
Config parameters:
mode: build
db_output: /data1/user/yuwq/haystac_db/yersinia_example
query: "Yersinia"[Organism] AND "complete genome"[All field]
bowtie2_scaling: 25.0
bowtie2_threads_db: 4
rank: species
cores: 40
mem: 191856
SyntaxError in line 9 of /data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/s3.py:
future feature annotations is not defined (s3.py, line 9)
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/init.py", line 34, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/smart_open_lib.py", line 35, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/doctools.py", line 21, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 104, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 49, in register_transport
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/importlib/init.py", line 126, in import_module
Even the basic example command cannot run correctly.
$ haystac database --mode build --query '"Yersinia"[Organism] AND "complete genome"[All field]' --output yersinia_example HAYSTAC v 0.4.10
Date: 2024-03-05 17:59:06.818678
Config parameters:
mode: build db_output: /data1/user/yuwq/haystac_db/yersinia_example query: "Yersinia"[Organism] AND "complete genome"[All field] bowtie2_scaling: 25.0 bowtie2_threads_db: 4 rank: species cores: 40 mem: 191856
SyntaxError in line 9 of /data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/s3.py: future feature annotations is not defined (s3.py, line 9) File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/init.py", line 34, in File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/smart_open_lib.py", line 35, in File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/doctools.py", line 21, in File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 104, in File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 49, in register_transport File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/importlib/init.py", line 126, in import_module
I've solved this problem by pip install smart_open==2.0.0pip install setuptools==49.6.0pip install pygments
Hello, when I try to build a database with accessions file, I met the error like this: --output [--query ]
[--query-file ] [--accessions-file ]
[--sequences-file ] [--refseq-rep ]
[--force-accessions]
[--exclude-accessions [ ...]]
[--resolve-accessions] [--bowtie2-scaling ]
[--bowtie2-threads ] [--rank ]
[--genera [ ...]] [--mtDNA]
[--seed ] [--batch ] [-h] [-v]
[--cores ] [--mem ] [--unlock] [--debug]
[--snakemake '']
haystac database: error: argument --accessions-file: 'pathogenlist1.txt' unknown error parsing file
Fishball99
commented
8 months ago
Fishball99
commented
8 months ago
Fishball99
commented
8 months ago
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haystac database --mode build --output pathogen --accessions-file pathogenlist1.txtusage: haystac database --modeHere' s some line in the pathogenlist1.txt accessions file: African_swine_fever_virus GCF_003032865.1 Aspergillus_fumigatus GCF_000002655.1 Bacillus_anthracis GCF_000008445.1 Bacillus_cereus GCF_002220285.1 Bartonella_bacilliformis GCF_000015445.1 Bartonella_henselae GCF_000612965.1 Bartonella_quintana GCF_021869585.1 Blastomyces_dermatitidis GCF_000003525.1 Bordetella_pertussis GCF_004008975.1 Bordetella_petrii GCF_000067205.1 Borreliella_afzelii GCF_018141305.1 Borreliella_burgdorferi GCF_000181575.2
list.txt
Even the basic example command cannot run correctly.
$ haystac database --mode build --query '"Yersinia"[Organism] AND "complete genome"[All field]' --output yersinia_exampleHAYSTAC v 0.4.10Date: 2024-03-05 17:59:06.818678
Config parameters:
mode: build db_output: /data1/user/yuwq/haystac_db/yersinia_example query: "Yersinia"[Organism] AND "complete genome"[All field] bowtie2_scaling: 25.0 bowtie2_threads_db: 4 rank: species cores: 40 mem: 191856
SyntaxError in line 9 of /data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/s3.py: future feature annotations is not defined (s3.py, line 9) File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/init.py", line 34, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/smart_open_lib.py", line 35, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/doctools.py", line 21, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 104, in
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/site-packages/smart_open/transport.py", line 49, in register_transport
File "/data1/user/yuwq/miniconda3/envs/haystac/lib/python3.6/importlib/init.py", line 126, in import_module
I've solved this problem by
pip install smart_open==2.0.0pip install setuptools==49.6.0pip install pygmentsI've successfully built the database by running the command with the argument ‘–accessions-file ./name_of_file.txt’