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

[Songq-20]

Dear BASALT team: Thank you for your efforts! In BASALT(v1.1.0), the previous problem has been resolved, but I have encountered a new problem: My commands:

export CHECKM2DB="/datanode03/huangxy/database/checkm_data/CheckM2_database/uniref100.KO.1.dmnd"

conda activate BASALT
a=2022_TGL_TJ3-4_megahit.contigs.fa
s1_1=TGL_TT1-2R1_trimmed.fq.gz
s1_2=TGL_TT1-2R2_trimmed.fq.gz
s2_1=TGL_TT3-4R1_trimmed.fq.gz
s2_2=TGL_TT3-4R2_trimmed.fq.gz
s3_1=TGL_TJ3-4R1_trimmed.fq.gz
s3_2=TGL_TJ3-4R2_trimmed.fq.gz
s4_1=TGL_TJ1-2R1_trimmed.fq.gz
s4_2=TGL_TJ1-2R2_trimmed.fq.gz
BASALT -a $a -s $s1_1,$s1_2/$s2_1,$s2_2/$s3_1,$s3_2/$s4_1,$s4_2 -t 20 -m 200 -q checkm2
conda deactivate

basalt.err :

Traceback (most recent call last):
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/ensemble.py", line 140, in <module>
    main(opt)
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/ensemble.py", line 30, in main
    dataset = MyDataSet_test(type=args.norm_type, use_256=args.use_256, fea=args.fea, split='test', dec=args.dec)
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/my_dataset.py", line 168, in __init__
    datas.append(norm(np.vstack(temp_datas), type))
UnboundLocalError: local variable 'temp_datas' referenced before assignment
Traceback (most recent call last):
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/BASALT", line 219, in <module>
    BASALT_main_d(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 "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/BASALT_main_d.py", line 456, in BASALT_main_d
    outlier_remover_main('BestBinset', coverage_matrix_list, datasets, lr_list, hifi_list, assembly_mo_list, pwd, num_threads)
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/S5_Outlier_remover_DL_11012023.py", line 549, in outlier_remover_main
    A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, lr, hifi_list, num_threads, nx)
  File "/data01nfs/user/songq/anaconda3/envs/BASALT/bin/S5_Outlier_remover_DL_11012023.py", line 145, in outlier_predictor
    for line in open('Predicted_potential_outlier.txt','r'):
FileNotFoundError: [Errno 2] No such file or directory: 'Predicted_potential_outlier.txt'

Basalt_checkpoint.txt ：

1st autobinner done!
2nd bin selection within group done!
3rd bin selection did not perform, because there is only one assembly!

Looking forward to your reply!

[vicru93]

Hi... Yes, the same thing happened to me

[sersancar]

Hi. I've found the same error after 1 month running the program over a huge dataset. Hope some reply.