An error in /SGVFinder2/cli/icra_cli.py file

[jiushao12345]

I have already build the refrence database. And I got anther error in ICRA step. It seems in the file (SGVFinder2/cli/icra_cli.py) This is a detailed error report: ..... 2024-01-16 16:46:50,779-INFO: Average read length for re_SF00036388_1_kneaddata_paired.fastq set to 148 2024-01-16 16:47:18,356-DEBUG: Method '_get_unique_cov_dic' took 0:00:00.000015 2024-01-16 16:47:18,356-INFO: _initialize: Parameter init complete. Time: 0:00:33.966127 this is the len of delta: 0 Finished running ICRA, saving results to /Gut_SV/test/test_3 Traceback (most recent call last): File "/minicoda3/envs/sgvfinder2/bin/icra", line 5, in from SGVFinder2.cli.icra_cli import main File "/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/cli/icra_cli.py", line 59, in print('Running get_sample_map on %s, output will be saved to'%(jsdel_file,jsdel_file.replace('.jsdel','.smp'))) TypeError: not all arguments converted during string formatting I check the icra_cli.py file, and I cannot found the command "import main" I changed the command "print('Running get_sample_map on %s, output will be saved to'%(jsdel_file,jsdel_file.replace('.jsdel','.smp')))" to "print('Running get_sample_map on %s, output will be saved to %s'%(jsdel_file,jsdel_file.replace('.jsdel','.smp')))". And I run the ICRA step again. This is the new error report: 2024-01-16 17:40:47,719-INFO: _initialize: Parameter init complete. Time: 0:00:31.487062 this is the len of delta: 0 Finished running ICRA, saving results to /Gut_SV/test/test_3 Running get_sample_map on /Gut_SV/test/test_3/re_SF00036388_1_kneaddata_paired.jsdel, output will be saved to /Gut_SV/test/test_3/re_SF00036388_1_kneaddata_paired.smp Traceback (most recent call last): File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/bin/icra", line 5, in from SGVFinder2.cli.icra_cli import main ImportError: cannot import name 'main' from 'SGVFinder2.cli.icra_cli' (/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/cli/icra_cli.py) I think there was something wrong in python file (SGVFinder2/cli/icra_cli.py) Thanks for your help.

[ym2877]

Hi @jiushao12345 please update the package to incorporate fix. Also note that you will need to install this package using pip install in order for these commands to work.

[jiushao12345]

Hi,@ym2877 It work well, thank you for your help. And I have another question now.