Error during pilon polish

[sulheim]

I tried to run Unicycler on a Virtual Box with Ubuntu 16.04, but it crashed during Pilon polish. Any idea what went wrong? Is it possible to continue the assembly, and only do the polishing?

Traceback (most recent call last): File "/usr/local/bin/unicycler", line 9, in <module> load_entry_point('unicycler==0.4.3', 'console_scripts', 'unicycler')() File "/usr/local/lib/python3.5/dist-packages/unicycler/unicycler.py", line 212, in main final_polish(graph, args, counter, long_reads_available) File "/usr/local/lib/python3.5/dist-packages/unicycler/unicycler.py", line 925, in final_polish polish_with_pilon_multiple_rounds(graph, graph, args, polish_dir, do_pilon_reassembly) File "/usr/local/lib/python3.5/dist-packages/unicycler/pilon_func.py", line 64, in polish_with_pilon_multiple_rounds insert_size_99th, i+1, fix_type) File "/usr/local/lib/python3.5/dist-packages/unicycler/pilon_func.py", line 335, in polish_with_pilon os.remove(f) OSError: [Errno 26] Text file busy: '1_pilon.changes'

[kapsakcj]

I too just ran into what I believe is the same issue you experienced. I believe it has to do with the fact that you're running it through VirtualBox. Check out this fix here, as it worked for me: #69 (comment)

[sulheim]

@kapsakcj sure? I encountered the Spades-issue as well, and changed the first line there, and that fixed the Spades-thing, but I thiink this is related to Pilon...

[kapsakcj]

@sulheim I apologize, I was confusing the two issues with one another. I too had both issues pop up when running Unicycler through VirtualBox.

The SPAdes fix worked for me, but I have not been able to figure out what is causing the issue with Pilon. So I too am looking for a solution!

[kapsakcj]

@sulheim I see from your original post that you are using unicycler v0.4.3. You may want to update to the current release (v0.4.4) and try running it again. I ran the current release of unicycler and did not see an error message during the pilon step as I saw before. YMMV

[sulheim]

Got the same error with Unicycler v0.4.4

[apredeus]

I didn't get the same error with 0.4.5, but Pilon was failing with "not enough memory" error when I ran it on 8-16 threads. You can go to pilon wrapper and change Java memory limit (Xmx) to 20 G or something else, depending on what your setup allows.

It might have nothing to do with memory though, it's hard to tell, since the error message you get is very uninformative.

[rrwick]

Hi @sulheim,

I don't really understand why this crash happened (or why it stopped happening in v0.4.5) but I've added an extra bit to catch the error, hopefully preventing such crashes in the future: 078a782. This is only in Unicycler's development branch now, but should make its way into the next release.

Regarding the memory issue and the wrapper suggestion @apredeus mentioned, you can find more info here: #63.

Hope that helps!
Ryan