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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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unicycler error while saving 005_bridges_applied.gfa #297

Open xzguqgsntdzq opened 2 years ago

xzguqgsntdzq commented 2 years ago

I'm getting the following error:

Saving /unicycler/005_bridges_applied.gfa Traceback (most recent call last): File "../unicycler-runner.py", line 21, in main() File "../unicycler.py", line 156, in main args.min_dead_end_size, graph, anchor_segments) File "../assembly_graph.py", line 1363, in clean_up_after_bridging_2 usedupness_scores[seg_num] = self.get_usedupness_score(seg_num, unbridged_graph) File "../assembly_graph.py", line 1526, in get_usedupness_score depth_fraction_used = depth_used / original_depth ZeroDivisionError: float division by zero

I'm getting the same error for a number of samples, each is Illumina+Nanopore reads.

My setup is: Unicycler version: v0.5.0 Program Version Status spades.py 3.14.0 good
racon 1.5.0 good
makeblastdb 2.11.0+ good
tblastn 2.11.0+ good

Any suggestions will be appreciated.

galaxychan commented 1 year ago

I got the same error.

I assembled the Illumina data and nanopore data. This "ZeroDivisionError" error occured in assembly process of one sample (the other four samples could execute right and get the assembly.fasta result). The output files was stopped with the file name "005_bridges_applied.gfa" and the log file just sudden end without recording any error message.

The error information was listed below:

Traceback (most recent call last): File "/usr/local/bin/unicycler", line 11, in load_entry_point('unicycler==0.5.0', 'console_scripts', 'unicycler')() File "/usr/local/lib/python3.6/site-packages/unicycler/unicycler.py", line 156, in main args.min_dead_end_size, graph, anchor_segments) File "/usr/local/lib/python3.6/site-packages/unicycler/assembly_graph.py", line 1363, in clean_up_after_bridging_2 usedupness_scores[seg_num] = self.get_usedupness_score(seg_num, unbridged_graph) File "/usr/local/lib/python3.6/site-packages/unicycler/assembly_graph.py", line 1531, in get_usedupness_score penalty = score_function(original_depth, 4.0) File "/usr/local/lib/python3.6/site-packages/unicycler/misc.py", line 377, in score_function return 1.0 - (half_score_val / (half_score_val + val)) ZeroDivisionError: float division by zero

Thank you a lot for any suggestion.

cmstouthamer commented 1 year ago

I have the same problem. Did you ever manage to figure this one out? I'm running version 0.5.0, same as above.