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churchill-lab / g2gtools

Personal diploid genome creation and coordinate conversion
http://churchill-lab.github.io/g2gtools
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Assertion error: start must be less than end #28

Open amkilpatrick opened 1 year ago

amkilpatrick commented 1 year ago

Hello, I'm trying to generate a diploid human reference genome following the standard workflow. Both g2gtools vcf2vci and g2gtools patch appear to run ok (~5M SNPs patched), but when I run 

g2gtools transform -i NA19670.patched.fa -c NA19670.vci.gz -o NA19670.fa -p 8 -d

I'm running into an exception:

Error Type: <type 'exceptions.AssertionError'>
Error Value: start must be less than end
<traceback object at 0x1544d2a279b0>
    /rds/general/user/akilpat1/home/anaconda3/envs/g2gtools_ml/lib/python2.7/site-packages/g2gtools-0.2.9-py2.7.egg/g2gtools/vci.py:299
    lib/bx/intervals/intersection.pyx:292

4 suggests something to do with chain files but as I understand this is for an older version of g2gtools?

As suggested in #19, I've refreshed the index files for both the patched.fa and vci files, but the result is the same. The chromosomes in both the patched.fa and VCI seem to be well-formed (1_L,1_R, etc), yet within the debug file there are lines such as:

[g2gtools debug] Chromosome 1_L not found in mapping tree
[g2gtools debug] Available chromsomes are: []
[g2gtools] This region was deleted
[g2gtools] TODO: dump the fasta sequence here

Any advice appreciated. Thanks!

mattjvincent commented 3 months ago

Please upgrade to g2gtools 2.0.0

Try:

docker run churchilllab/g2gtools:2.0.0 g2gtools --help