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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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IndexError: list index out of range syri #254

Closed lifannn11 closed 2 months ago

lifannn11 commented 3 months ago

Hi: When I run syri, some of them can successfully run, but some encounter a problem. I've tried for a long time but still can't solve it. Does anyone know how to fix it? image

lrauschning commented 3 months ago

Hi @lifannn11 can you be more specific as to how you are calling syri, and when it runs for you/when it produces the error in the screenshot?

lifannn11 commented 3 months ago

Hi @lifannn11 can you be more specific as to how you are calling syri, and when it runs for you/when it produces the error in the screenshot?

Hi: Here are the specific details. syri --nc 10 --nosnp --prefix SV. -c newout.mcoords -d newout.mdelta -r ref.fa -q order.qry.fasta image

Thanks

lrauschning commented 3 months ago

And which samples fail for you vs which ones run successfully? Sorry, from the screenshot I don't really know what is failing here. Is there any other output, or something printed to the log file (should be syri.log with how you're calling it)?

lifannn11 commented 3 months ago

哪些样本失败了，哪些样本成功运行了？对不起，从屏幕截图中我真的不知道这里有什么失败。是否有任何其他输出，或者打印到日志文件的内容（应该与你的调用方式相同）？syri.log

Hello, this is the generated SV.syri.log file. SV.syri.log

Thanks.

mnshgl0110 commented 3 months ago

Hi @lifannn11, This issue is typically caused when the genomes have different strands for homologous chromosomes (https://github.com/schneebergerlab/syri/issues/48). Have you checked whether for the homologous chromosomes the assemblies have the same strand? You can try plotting a dotplot using fixchr to check that.

mnshgl0110 commented 3 months ago

Hi @lifannn11. From the dotplots, it seem that the genomes are highly rearranged/diverged. As a result, fixchr could not orient them the chromosomes. All of the chromosomes look in correct orientation, except chr09. You can try reverse complementing Chr09 in the query genome manually and then realign and rerun syri.

hyBio commented 3 months ago

If I want to compare more than 2 genomes at the same time, when they are inverted that means I need to run fixchr twice. Some chromosomes will be inverted twice. I don't think that using fixchr is a good solution.

mnshgl0110 commented 2 months ago

@hyBio Please start a new issue for questions that are not related to the original posts. fixchr inverts only the query genomes. So, aligning multiple genomes to a reference genome and then running fixchr should orient all chromosomes.

mnshgl0110 commented 2 months ago

@lifannn11 I am not sure I understand your question. If you are unsure how to interpret dotplots, then maybe read some guides present online (like this: https://omicstutorials.com/interpreting-dot-plot-bioinformatics-with-an-example/). In the dotplots generated by fixchr, the alignments near the bottom-left to top-right diagonal corresponds to syntenic/directed alignments, while those near the top-left to bottom-right diagonals are inverted.