Error in test with metabinner

[corkdagga]

Hi,

Thank you for the great tool! I hope to eventually use it in my pipeline if I can get it to work correctly :)

I have installed BASALT using the recommended workflow and I think I upgraded it to V1.1.0 by downloading the scripts and copying them into the BASALT/bin folder (but actually, I am not sure which version I am running because I don't know how to check or find that....)

Anyway, I add the '-e m' command to the BASALT_test.sh script and get the following error:

usage: ensemble.py [-h] [--norm_type {mmn,absmmn,none}] [--use_256 USE_256]
                   [--fea FEA] [--dec DEC] [--mode MODE] [--ckpt_dir CKPT_DIR]
                   [--url_prefix URL_PREFIX] [--num_classes NUM_CLASSES]
                   [--batch_size BATCH_SIZE] [-o OUTPUT] [--device DEVICE]
ensemble.py: error: unrecognized arguments: /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/unitem_profile/binning_methods/X_t_logtrans_ori/checkm_bac/marker_gene_table.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/unitem_profile/binning_methods/X_t_logtrans_ori/checkm_ar/marker_gene_table.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/intermediate_result/2postprocess_X_cov_logtrans_bins_dir.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/X_cov_logtrans_2postprocess
cp: cannot stat '/home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/X_t_logtrans_2postprocess/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
cp: cannot stat '/home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/X_cov_logtrans_2postprocess/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
cp: cannot stat '/home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/X_com_logtrans_2postprocess/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
ls: cannot access 'X_t_logtrans_greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
ls: cannot access 'X_t_logtrans_greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
ls: cannot access 'X_t_logtrans_greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
ls: cannot access 'X_t_logtrans_greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins': No such file or directory
usage: ensemble.py [-h] [--norm_type {mmn,absmmn,none}] [--use_256 USE_256]
                   [--fea FEA] [--dec DEC] [--mode MODE] [--ckpt_dir CKPT_DIR]
                   [--url_prefix URL_PREFIX] [--num_classes NUM_CLASSES]
                   [--batch_size BATCH_SIZE] [-o OUTPUT] [--device DEVICE]
ensemble.py: error: unrecognized arguments: /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/unitem_profile/binning_methods/X_t_logtrans_ori/checkm_bac/marker_gene_table.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/unitem_profile/binning_methods/X_t_logtrans_ori/checkm_ar/marker_gene_table.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins/ensemble_3logtrans/addrefined2and3comps_bins_dir.tsv /home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/ensemble_res/greedy_cont_weight_3_mincomp_50.0_maxcont_15.0_bins/ensemble_3logtrans/addrefined2and3comps
Something went wrong with running ensemble.py. Exiting.
Traceback (most recent call last):
  File "/home/lab/miniforge3/envs/BASALT/bin/BASALT", line 241, in <module>
    BASALT_main_c_autobinning(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, sensitivity, refinement_paramter, max_ctn, min_cpn, pwd, QC_software, output_folder)
  File "/home/lab/miniforge3/envs/BASALT/bin/BASALT_main_c_autobinning.py", line 264, in BASALT_main_c_autobinning
    extra_bin_folder=extra_binner(binner, datasets, assembly_file, depth_file, num_threads, ram, pwd, QC_software)
  File "/home/lab/miniforge3/envs/BASALT/bin/S1e_extra_binners.py", line 130, in extra_binner
    metabinner(assembly_file, depth_file, num_threads, ram, pwd, QC_software)
  File "/home/lab/miniforge3/envs/BASALT/bin/S1e_extra_binners.py", line 50, in metabinner
    for line in open(pwd+'/'+str(assembly_file)+'_metabinner/metabinner_res/metabinner_result.tsv','r'):
FileNotFoundError: [Errno 2] No such file or directory: '/home/lab/tools/BASALT/22323424/1_assembly.fa_metabinner/metabinner_res/metabinner_result.tsv'

When running the script without metabinner, it works correctly.

I would really like to include metabinner, is there a way to fix this error?

Also, is there a way to identify which version of BASALT I am running?

Thanks!

[Lei93]

Hi, have you got the solution? I also have the same error.

[ucaswhw]

I also have the same error.

[zhaorui-bi]

BASALT v.1.2.0 now not support metabinner. However, BASALT v1.1.0 only provide metabinner inerface. If there has any problem, it is a good idea to ask the issue area in metabinner https://github.com/ziyewang/MetaBinner