I tried running with the test data and got the following issue:
K-mer analysis started...
Traceback (most recent call last):
File "/usr/local/bin/tandemquast", line 145, in
main()
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/local/bin/tandemquast", line 117, in main
kmer_analysis.do(assemblies, reads_fname, out_dir, no_reuse)
File "/home/ubuntu/TandemTools/scripts/kmer_analysis.py", line 156, in do
f.write("Single clump\t%.2f (%d)\n" % (len(one_clump)*100.0/all_kmers,len(one_clump)))
ZeroDivisionError: float division by zero
my command was:
tandemquast --nano TandemTools/test_data/simulated_reads.fasta TandemTools/test_data/simulated_polished.fa -o TandemTools/test_data/simulated_res -t 16
I also tried to run it without the --only-polish flag and got this error:
Analyzing simulated-polished assembly
Traceback (most recent call last):
File "/usr/local/bin/tandemquast", line 145, in
main()
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/ubuntu/miniconda3/envs/flye/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/local/bin/tandemquast", line 89, in main
polishing.do(assemblies, reads_fname, hifi_reads_fname, out_dir, tmp_dir)
File "/home/ubuntu/TandemTools/scripts/polishing.py", line 29, in do
select_kmers.do(assemblies, reads_fname, reads_fname, hifi_reads_fname, out_dir, tmp_dir, no_reuse=True, only_polish=True)
File "/home/ubuntu/TandemTools/scripts/select_kmers.py", line 156, in do
max_occ_in_assembly = max(1, get_fasta_len(assembly_fname) // 100000)
TypeError: unsupported operand type(s) for //: 'NoneType' and 'int'
ablab
