empty fasta file:'Remapping.fasta'; local variable 'bam_sorted' referenced before assignment

[FengqingWang0712]

Hello,
First, thank you for this cool tool.
However, I got this error. It's the latest version by the way. Can you help me with it?
Input files DNA, FASTA:
Remapping.fasta
Warning: Empty fasta file: 'Remapping.fasta'
Warning: All fasta inputs were empty
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/bowtie2-build-s --wrapper basic-0 Remapping.fasta Remapping.fasta
Traceback (most recent call last):
File "/bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/S5_Outlier_remover_DL_checkm.py", line 289, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/BASALT", line 141, in
BASALT_main_c(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software)
File "/bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/BASALT_main_c.py", line 441, in BASALT_main_c
outlier_remover_main('BestBinset', coverage_matrix_list, datasets, assembly_mo_list, pwd, num_threads)
File "/bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/S5_Outlier_remover_DL_checkm.py", line 452, in outlier_remover_main
A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, num_threads, nx)
File "/bioinf/home/fwang/software/miniconda3/envs/BASALT-1.1.0/bin/S5_Outlier_remover_DL_checkm.py", line 296, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment

[noddevil4949]

Hi,

It looks like that there is no fasta file generated in the previous step. Could you please have a check the content in the "BestBinset" folder? If this folder is empty, it means you have either encountered an error at the previous step, or even earlier.

Cheers,
BASALT team

[FengqingWang0712]

Thank you for your reply.
The "BestBinset" folder is not empty. Actually it includes many refined bins and statistic files with bins' quality.

Best

[noddevil4949]

Hmm it looks weird. Could you please add my Wechat "noddevil4949" so we can have a look at details?

[Eirwyn-sheen]

Hello, I encounter a similar problem. Can you help me?
Order: BASALT -a asm.p_ctg.fasta -hf ~/share/xmc_seq/xmc_hifi_reads.fq.gz -t 60
Input files DNA, FASTA:
Remapping.fasta
Warning: Empty fasta file: 'Remapping.fasta'
Warning: All fasta inputs were empty
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/bowtie2-build-s --wrapper basic-0 Remapping.fasta Remapping.fasta
Predicting potential outliers
Judging 1_asm.p_ctg.fasta_100_concoct_genomes.21.fasta
Judging 1_asm.p_ctg.fasta_200_concoct_genomes.29.fasta
Judging 1_asm.p_ctg.fasta_200_concoct_genomes.18.fasta
Judging 1_asm.p_ctg.fasta_200_concoct_genomes.8.fasta
Judging 1_asm.p_ctg.fasta_0.9_maxbin2_genomes.5.fasta
Judging 1_asm.p_ctg.fasta_0.9_maxbin2_genomes.6.fasta
Judging 1_asm.p_ctg.fasta_0.9_maxbin2_genomes.7.fasta
Judging 1_asm.p_ctg.fasta_100_concoct_genomes.22.fasta
Judging 1_asm.p_ctg.fasta_200_concoct_genomes.25.fasta
Re-mapping
Traceback (most recent call last):
File "/home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 289, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/BASALT", line 141, in
BASALT_main_c(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software)
File "/home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/BASALT_main_c.py", line 441, in BASALT_main_c
outlier_remover_main('BestBinset', coverage_matrix_list, datasets, assembly_mo_list, pwd, num_threads)
File "/home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 452, in outlier_remover_main
A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, num_threads, nx)
File "/home/wangbx/xxq_xmc/bin/mimcromamba/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 296, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment

[mnter]

Hello,
I have met a similar problem "UnboundLocalError: local variable 'bam_sorted' referenced before assignment".
But in my case, the Remapping.fasta file was indexed successively.
Also, the "BestBinset" folder is not empty.
Has the problem been solved?
Thank you

Total time for backward call to driver() for mirror index: 00:00:23
Renaming Remapping.fasta.3.bt2.tmp to Remapping.fasta.3.bt2
Renaming Remapping.fasta.4.bt2.tmp to Remapping.fasta.4.bt2
Renaming Remapping.fasta.1.bt2.tmp to Remapping.fasta.1.bt2
Renaming Remapping.fasta.2.bt2.tmp to Remapping.fasta.2.bt2
Renaming Remapping.fasta.rev.1.bt2.tmp to Remapping.fasta.rev.1.bt2
Renaming Remapping.fasta.rev.2.bt2.tmp to Remapping.fasta.rev.2.bt2
Traceback (most recent call last):
File "/home/sophy/mambaforge/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 289, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/sophy/mambaforge/envs/BASALT/bin/BASALT", line 141, in
BASALT_main_c(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software)
File "/home/sophy/mambaforge/envs/BASALT/bin/BASALT_main_c.py", line 441, in BASALT_main_c
outlier_remover_main('BestBinset', coverage_matrix_list, datasets, assembly_mo_list, pwd, num_threads)
File "/home/sophy/mambaforge/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 452, in outlier_remover_main
A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, num_threads, nx)
File "/home/sophy/mambaforge/envs/BASALT/bin/S5_Outlier_remover_DL_checkm.py", line 296, in outlier_predictor
os.system('jgi_summarize_bam_contig_depths --outputDepth Re-mapped_depth.txt '+str(bam_sorted))
UnboundLocalError: local variable 'bam_sorted' referenced before assignment