IndexError: list index out of range

[jrherr]

This appears to be similar to issue #5, but I am getting this error:

Final shred and polish (2019-09-09)
    To get the best possible consensus, Rebaler now shreds the previous
polished assemblies to make "reads" for a final couple rounds of polishing.

Traceback (most recent call last):
  File "/Users/user/anaconda3/bin/rebaler", line 11, in <module>
    load_entry_point('Rebaler==0.2.0', 'console_scripts', 'rebaler')()
  File "/Users/user/anaconda3/lib/python3.7/site-packages/Rebaler-0.2.0-py3.7.egg/rebaler/__main__.py", line 97, in main
  File "/Users/user/anaconda3/lib/python3.7/site-packages/Rebaler-0.2.0-py3.7.egg/rebaler/__main__.py", line 171, in final_shred_and_polish
IndexError: list index out of range

I've tried 3 different datasets (with their respective references) on two different computers (Mac OSX High Sierra and Ubuntu 18.04.3 LTS) with both racon 1.3.1 and 1.3.2_1. Minimap2 is working properly. All variations produce the same error message.

Any ideas on how to fix this issue? Thanks!

[camilogarciabotero]

Hi @rrwick,

I see I got the same error as @jrherr: I was running Rebaler for building a reference based assembly with PacBio fastq files. It starts good with Minimap and then with Racon. However, when it starts the polishing round and the final "shredding" it gives me the following error:

So, if you can give any solution or suggest me another cool tool for reference based genome assembly I will be very thankful. Or if @jrherr could solved this problem It would be pretty good to sort this out.

Cheers.

[mbhall88]

I have also recently run into this issue. It looks like you're both using the bioconda version of Rebaler?

My suspicion is that Racon is failing (there have been issues with the Racon bioconda recipe in the past) multiple times, and thus Rebaler is giving up and not returning any assemblies. The most recent version of Racon should hopefully fix these problems.
I found that running multiple times, I eventually got the failing jobs to succeed.

If you are still getting this problem with a fresh conda install of Rebaler, I would suggest trying to install the latest version of Racon first (version >=1.4.12), and then install Rebaler. The Rebaler conda recipe doesn't pin a version of Racon, so it should install the latest - but check this in the install log. I will additionally put in a PR to bioconda to update the Racon version required by Rebaler.

I hope this helps and it's not just a useless rant.

[camilogarciabotero]

Hi @mbhall88,

Yes, I did install Rebaler using bioconda. When running Rebaler before I can't recall what version of Racon I was using, however I updated my Conda environments several times and Rebaler ended up working pretty good. I've just checked the Racon version and it is 1.14.13.

Thank you for your comment!
Cheers.