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svim2.0.0 err

Open vegetableyu opened this issue 1 year ago • 0 comments

Hi, i am using svim2.0.0 and encountered an err: [ERROR ] '<' not supported between instances of 'NoneType' and 'str' Traceback (most recent call last): File "/miniconda3/envs/svcaller/bin/svim", line 221, in sys.exit(main()) File "/miniconda3/envs/svcaller/bin/svim", line 132, in main signature_clusters = cluster_sv_signatures(sv_signatures, options) File "/miniconda3/envs/svcaller/lib/python3.9/site-packages/svim/SVIM_CLUSTER.py", line 19, in cluster_sv_signatures deletion_signature_clusters = partition_and_cluster(deletion_signatures, options, "deleted regions") File "/miniconda3/envs/svcaller/lib/python3.9/site-packages/svim/SVIM_clustering.py", line 376, in partition_and_cluster partitions = form_partitions(signatures, options.partition_max_distance) File "/miniconda3/envs/svcaller/lib/python3.9/site-packages/svim/SVIM_clustering.py", line 19, in form_partitions sorted_signatures = sorted(sv_signatures, key=lambda evi: evi.get_key()) TypeError: '<' not supported between instances of 'NoneType' and 'str'

The command is : svim alignment --min_sv_size 50 --sample {sample} {inputbam} {inputfa}

Look forward to your kind reply. YU

vegetableyu avatar Dec 20 '23 08:12 vegetableyu