AttributeError: 'str' object has no attribute 'append'

[wangzefei446]

hello,when I run the prepare.py,I got this problem,how can I solve it? Traceback (most recent call last): File "/share/home/bgi_cwangzf/softare/AvP/depot/prepare.py", line 34, in from depot.PetIO import check_programs, get_outdir, progress, open_file File "/share/home/bgi_cwangzf/miniconda3/lib/python3.10/site-packages/depot/init.py", line 25, in from .storage import StorageWrapper File "/share/home/bgi_cwangzf/miniconda3/lib/python3.10/site-packages/depot/storage.py", line 13, in libcloud.security.CA_CERTS_PATH.append(os.path.join(_base_path, 'cacert.pem')) AttributeError: 'str' object has no attribute 'append'

[GDKO]

Hi @wangzefei446,

Can you share your prepare command and your config file?

Cheers, Georgios

[wangzefei446]

Hi @wangzefei446,

Can you share your prepare command and your config file?

Cheers, Georgios this is command: /share/home/bgi_cwangzf/softare/AvP/depot/prepare.py -a 126.out_ai.out -o /share/home/bgi_cwangzf/database/NR/126 -f 126.faa -b 126.out -x groups.yaml -c config.yaml this is config.file

max_threads: 48

DB path

blast_db_path: /share/appspace_data/shared_groups/BGI/02.DataBase/NR_220531 # blast: change to the local blast_db path fasta_path: /share/appspace_data/shared_groups/BGI/02.DataBase/NR_220531/Baceria.fa # 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 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: 12

[GDKO]

Please take a look at the wiki on how to properly run the software

/share/home/bgi_cwangzf/softare/AvP/depot/prepare.py -a 126.out_ai.out -o /share/home/bgi_cwangzf/database/NR/126 -f 126.faa -b 126.out -x groups.yaml -c config.yaml

Your command should be like this

/share/home/bgi_cwangzf/softare/AvP/avp prepare -a 126.out_ai.out -o /share/home/bgi_cwangzf/database/NR/126 -f 126.faa -b 126.out -x groups.yaml -c config.yaml

Also another issue, I have noticed that you provide a fasta_path together with your blast_db_path, and I am guessing that NR_220531 is a directory.

Before continuing what was your blast command?

[wangzefei446]

Please take a look at the wiki on how to properly run the software

/share/home/bgi_cwangzf/softare/AvP/depot/prepare.py -a 126.out_ai.out -o /share/home/bgi_cwangzf/database/NR/126 -f 126.faa -b 126.out -x groups.yaml -c config.yaml

Your command should be like this

/share/home/bgi_cwangzf/softare/AvP/avp prepare -a 126.out_ai.out -o /share/home/bgi_cwangzf/database/NR/126 -f 126.faa -b 126.out -x groups.yaml -c config.yaml

Also another issue, I have noticed that you provide a fasta_path together with your blast_db_path, and I am guessing that NR_220531 is a directory.

Before continuing what was your blast command?

Excuse me, I'll ask you a question，the blast_db_path is nr_blast_db_path,the fasta_path，what does it refer to？

[GDKO]

• If you use NR the recommendation is to use blast against it and set the blast_db_path to your NR database path (the same as your blast command [-db option]).
• If you use other databases the recommendation is to use diamond with some specific formatting. Then you set the fasta_path to your database fasta file.

You can read more here.