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EMBL-PKU / BASALT

MIT License
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Only use contig #20

Closed wangyujie000 closed 3 months ago

wangyujie000 commented 3 months ago

I only wanted to use contigs to run, and the command was “BASALT -a 1.fasta -t 20 -m 120” Here is error: Traceback (most recent call last): File "/home/xxx/mambaforge-pypy3/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/xxx/mambaforge-pypy3/envs/BASALT/bin/BASALT_main_c.py", line 258, in BASALT_main_c A=autobinner_main(assembly_list, datasets, lr_list, hifi_list, insert_size, num_threads, ram, autobining_parameters, QC_software, pwd) File "/home/xxx/mambaforge-pypy3/envs/BASALT/bin/S1_Autobinners_2qc_11152023.py", line 1109, in autobinner_main bam_sorted=bam_sorted2 UnboundLocalError: local variable 'bam_sorted2' referenced before assignment Is there a solution? Or it has to be with SR dataset? Thank you!

noddevil4949 commented 3 months ago

Hi,

Raw fasta files are essential to calculate the depth of contigs, therefore binning cannot proceed without raw reads. Please have another go once you have raw reads ready. Thanks for using BASALT!

Cheers