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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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getTSV - ERROR - Error in finding parent for SNP getTSV - ERROR - # 566892 2624868 1 2058353 chr01 chr1 Series([], ) #194

Closed karrysorry closed 1 year ago

karrysorry commented 1 year ago

Hello，Manish Goel. I'm running syri with the delta file of two species using nucmer. The following is my command line: nucmer --prefix=name ref.Chr.fasta query.Chr.fasta -p out -t 20 delta-filter -1 -l 100 out.delta > m_i90_l100.delta show-coords -THrd yy92.delta.filiter > [yy92.delta.filiter.coords python3 syri -c yy92.delta.filiter.coords -d yy92.delta.filiter -r ref.Chr.fasta -q query.Chr.fasta -k --prefix=name -s show-snps --lf name.log

and I'm getting this error: getTSV - ERROR - Error in finding parent for SNP getTSV - ERROR - # 566892 2624868 1 2058353 chr01 chr1 Series([], )

Any way to resolve this issue?

Thanks.

sincerely Karrysorry

mnshgl0110 commented 1 year ago

Can you try running syri in a new directory containing only the .fasta, .delta, and .coords file? If that does not work, please run syri with the log level set to debug and then share the syri.log file.

karrysorry commented 1 year ago

Okay, thanks, I ran Nucmer again before and the results are not yet in. After the results come out, I will try your method. Again, express my sincere gratitude.

sincerely Karrysorry

karrysorry commented 1 year ago

I followed your method and the result has already run out, thank you

sincerely Karrysorry

karrysorry commented 1 year ago

However, a new error has occurred。 Running SyRI - ERROR - :202 - Length of reference sequence of chr10 is less than the maximum coordin ate of its aligned regions. Exiting.