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base.py line 34, in make_ranges q, s, t = zip(*ib) -- ValueError: not enough values to unpack (expected 3, got 0) #690
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Thanks for reporting the issue and sending the data to debug. You are correct that the empty block is the issue here. ###
evm.model.Chr4.5631 mrna.AA559650.t1 919
evm.model.Chr4.5633 mrna.AA559640.t1 1600
evm.model.Chr4.5634 mrna.AA559630.t1 571
###
- evm.model.Chr4.7694 mrna.AA560110.t1 2300
- evm.model.Chr4.7694 mrna.AA560120.t1 1410
###
evm.model.Chr4.1717 mrna.AA564650.t1 1210
evm.model.Chr4.1718.1 mrna.AA564640.t1 389 This is the removed block. Why is it removed is a little complicated. You can skip the below if TLDR; When JCVI processes the LAST output, it tries to identify likely tandem genes since their presence will inflate the # of syntenic anchors. In the initial LAST output, there were two pairs:
These get converted to:
since JCVI considers Normally, this would be okay, but, since LAST is not transitive, this can lead to non-existent LAST pairs (for example, if I'll have a fix for that empty block soon. |
* debug bp seq * Do not keep empty blocks (#690, thanks @Tong-Chen) * Add test_empty_blocks * move filter_blocks outside print_to_file
Thanks! |
When running
python -m jcvi.compara.synteny mcscan Bbalcxl0706.bed Bbalcxl0706.Aan1.lifted.anchors --iter=100 -o Bbalcxl0706.Aan1.blocks.txt
, I met the error below:I added
print(id)
beforeq, s, t = zip(*ib)
in/anaconda3/envs/jcvi/lib/python3.10/site-packages/jcvi/compara/base.py"
, and got the empty list which caused the error.I could add an if test to skip empty items. However, I do not know why there is an empty block.
Then I checked the input file with the context neighboring
evm.model.Chr4.5634
(the block just before the empty block)In
Bbalcxl0706.Aan1.lifted.anchors
I do not know if this is caused by the
###\n###
? And why do we get these double comment lines?The command used to generate the anchors:
Thanks!
Tong
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