IndexError: list out of range

[Kata-Pa]

Hello,

I just tried your tool, which looks quite useful, and everything runned fine until I got the following error:
File "/home/katerina87/miniconda3/bin/get_organelle_from_reads.py", line 3482, in main
expected_maximum_size=options.expected_max_size[go_t],
IndexError: list index out of range

The command I run was

get_organelle_from_reads.py -1 VM3-16_S1_R1.pick.fastq -2 VM3-16_S1_R2.pick.fastq -s Chloroplast.pick.fasta -o GetO_S1_assembly -F other_pt

The reference fasta I am using is from the same species.

Any help or hint on the error would be very helpful.
Thank you!

[Kinggerm]

Sorry for the late reply and the inconvenience caused by this issue.
Please see #13 for a temporary solution.
Alternatively, update to 1.6.2 (on the way).

Cheers!

[Kinggerm]

1.6.2 released. You can now either use the removing dep way or update GetOrganelle to solve this problem.

[Kata-Pa]

Ok will try the update, thank you for the fast reply :)

[Kata-Pa]

So I updated but I still get the same error. I also noticed that the script is running from the bin in miniconda while I had done a pip3 install. I rerun using the script in my pip installed folder but still get the same error. So maybe conda and pip conflict is not the problem? Also deleted the ncbi-blast folder and reinstall, same error.
Could it be a problem of my input then?

[Kinggerm]

Could be the conflict.
Can you show me the complete log file from which I can understand the environment you are using?
I don't think it's the problem with any of your input.

[Kata-Pa]

get_org.log.txt

Here it is

[Kinggerm]

Sorry, my fault!!!! Eyes spent ...
It should not be the same issue with #13. I would look into this right now and get back to you soon.

[Kinggerm]

Thank you very much for pointing out this bug! I got it. I missed the other_pt mode in a few code lines and barely tested it. It is interesting that you are using GetOrganelle to assemble plastomes of non-embryophytes.

Fixed now! Please update GetOrganelle, again.
BTW, You can add "--continue" to the commands to quickly resume the previous run. Please let me know what you get.

[Kinggerm]

It seems that you did not get many original reads but with extremely high pt percentage. Was it purified DNA or something?

[Kata-Pa]

Thank you Jianjun!
I need to assemble the chloroplast of a diatom (phytoplankton). The genome is already known, so I mapped the raw reads and extracted only the ones matching to the chloroplast contig. Now will use your tool to assemble the chloroplast for the different strains I have. Hope it works nicely!
Thank you once more for your fast reply.

[Kinggerm]

No problem!
You can do the mapping then use GetOrganelle if it is extremely close samples and the result says complete. However, to avoid incomplete result or bias, use GetOrganelle to assemble the plastome from the original reads would be much more preferred.