agshumate/Liftoff

-polish giving IndexError: list index out of range

Closed this issue · 15 comments

afbent commented

Thank you for the excellent software.
Liftoff has worked well for me (maps gene calls onto new genome) if I leave out the -polish command. But of course I want to polish the liftoff results because I am mapping onto a (very similar, same species but) different genome.

Running:
liftoff -g htype2-DNewF-genecalls.sorted.gff3 -o htype2-DNewF-polishedGeneCalls.gff3 -f lift_features.txt -dir liftoff_intermed_files -polish -p 24 htype2-DipphasedNewFinal.fasta Cam_Hsc_genome1.2.fa.bak

Here is the liftoff screen output (aligning and lifting finish, polish does not):

aligning features
lifting features
polishing annotations
Traceback (most recent call last):
File "/home/ab2835/anaconda3/envs/WHparpil/bin/liftoff", line 10, in
sys.exit(main())
File "/home/ab2835/anaconda3/envs/WHparpil/lib/python3.8/site-packages/liftoff/run_liftoff.py", line 10, in main
run_all_liftoff_steps(args)
File "/home/ab2835/anaconda3/envs/WHparpil/lib/python3.8/site-packages/liftoff/run_liftoff.py", line 40, in run_all_liftoff_steps
find_and_polish_broken_cds(args, lifted_feature_list,feature_hierarchy, ref_chroms,
File "/home/ab2835/anaconda3/envs/WHparpil/lib/python3.8/site-packages/liftoff/run_liftoff.py", line 244, in find_and_polish_broken_cds
aligned_segments_new[target_feature] = list(aligned_segments.values())[0]
IndexError: list index out of range

Same error occurred when using original gff3 file generated by Augustus using gtf2gff.pl, or using as input the gff3 output file generated by a previous liftoff run that did not include the -polish option.

Any suggestions appreciated.

agshumate commented

Hi there,
Which version of liftoff are you using?

afbent commented
agshumate commented

sorry for the delay, is it possible for you to share your input files with me?

afbent commented
agshumate commented

if you have an ftp site that they can be uploaded to, that would be the easiest. otherwise i can provide details on sharing to our ftp site. thanks.

SchwarzEM commented

I have encountered what appears to be the same problem (getting an "IndexError: list index out of range" error message if I use -polish in LiftOff, with this error arising immediately after the 'polishing annotations' step of my analysis). Has this issue been corrected yet? The version of LiftOff I am using is 1.6.1, installed via bioconda.

agshumate commented

HI there,
apologies for the delayed response. Do you have any test data I can use to debug this issue?

mariasilviamorlino commented

I have encountered the exact same error, using v1.6.1 installed with bioconda as well. I would be happy to share my input data to your ftp.

agshumate commented

great, if you could provide me your email address i can send you instructions for uploading to our ftp

agshumate commented

hello all,
thanks for your patience. it turns out that the latest commit on the master branch already has a fix for this issue. please update to the latest commit and let me know if you have further issues

SchwarzEM commented

"The latest commit on the master branch" requires, I assume, installation as follows:

git clone https://github.com/agshumate/Liftoff liftoff 
cd liftoff
python setup.py install

Can this updated version be exported to bioconda as a package?

agshumate commented

the updated version is now available on bioconda (v1.6.2). apologies for the delay!

afbent commented
Czirion commented

Hello,
I am encountering the same error while using v1.6.3

  • 👍1