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EMBL-PKU / BASALT

MIT License
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The issue of CheckM #2

Closed Yanh35 closed 6 months ago

Yanh35 commented 2 years ago

When I tried to run this code, I got the following problem: ''' File "BASALT/BASALT_main.py", line 361, in BASALT_main contig_outlier_remover_main('BestBinset', coverage_matrix_list, connections_list, num_threads, ram) File "BASALT/S5_Outlier_remover_mpt_05162022.py", line 1335, in contig_outlier_remover_main bin_comparison(best_binset_from_multi_assemblies+'_coverage_refined', best_binset_from_multi_assemblies+'_TNFs_refined', 'fa', 'TNFs', num_threads, ram, pwd) File "BASALT/S5_Outlier_remover_mpt_05162022.py", line 722, in bin_comparison os.chdir(refined_binset+'_checkm/storage/') FileNotFoundError: [Errno 2] No such file or directory: 'BestBinset_TNFs_refined_checkm/storage/' ''' I also checked the file "BestBinset_TNFs_refined_checkm/checkm.log", it showed that ''' INFO: CheckM v1.1.3 INFO: checkm lineage_wf -t 40 -x fa BestBinset_TNFs_refined BestBinset_TNFs_refined_checkm INFO: [CheckM - tree] Placing bins in reference genome tree. ERROR: No bins found. Check the extension (-x) used to identify bins. '''

EMBL-PKU commented 2 years ago

Thanks for using BASALT. We have fixed this error. You can try running again.