output_tsv issue

[XingshuaiCui]

Traceback (most recent call last):
File "/opt/anaconda3/envs/antismash/bin/bigslice", line 1960, in
return_code = main()
^^^^^^
File "/opt/anaconda3/envs/antismash/bin/bigslice", line 1850, in main
store_pickle(bgc_features, pickled_file_path)
File "/opt/anaconda3/envs/antismash/lib/python3.11/site-packages/bigslice/modules/utils.py", line 77, in store_pickle
with open(pickle_path, "wb") as fp:
^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/metagenome/test_out/result/cache/bgc_features_1.pkl'

[MdUmar-tech]

The error happened because:

You are using antiSMASH 8, but the software (probably BiG-SLiCE or another tool) was made for antiSMASH 7 outputs.

The .gbk files have a header line like:
Version :: 8.

so Solution is
You can change:

Version :: 8.
to
Version :: 7.
in all .gbk files.

✅ If you have many .gbk files, use this Python script:

def convert_only_version(gbk_file):
    with open(gbk_file) as f:
        content = f.read()

    # Only change version line
    content = content.replace("Version     :: 8.", "Version      :: 7.")

    return content

import os

gbk_folder = "./dataset_1/dataset_1/NC_003888.3"

for filename in os.listdir(gbk_folder):
    if filename.endswith(".gbk"):
        filepath = os.path.join(gbk_folder, filename)
        new_content = convert_only_version(filepath)
        with open(filepath, "w") as f:
            f.write(new_content)
        print(f"Fixed version in {filename}")

This will go through all .gbk files in the folder and replace the version line. After this, you can rerun your pipeline.