[Errno 2] No such file or directory: 'Coverage_matrix_list.txt'

[corkdagga]

Hi Again!

For the most part, I have got BASALT to work nicely on some of my metagenomes. During my BASALT runs, I sometimes get the error shown below. However, when I resume/repeat the run (identical command but changing --mode new --> --mode continue) it seems to work correctly after that with BASALT binning running to completion.

rm: cannot remove 'TNFs_exceptional_contigs.txt': No such file or directory
rm: cannot remove 'Total_contigs_after_OLC_reassembly.fa': No such file or directory
BASALT started from step: 0
Starting outlier removal process
Traceback (most recent call last):
  File "/home/lab/miniforge3/envs/BASALT/bin/BASALT", line 245, in <module>
    BASALT_main_c_refinement(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_refinement.py", line 246, in BASALT_main_c_refinement
    for line in open('Coverage_matrix_list.txt','r'):
FileNotFoundError: [Errno 2] No such file or directory: 'Coverage_matrix_list.txt'