IndexError: list index out of range(direction) about syri HOT 6 CLOSED

Hi @Pengzw0909. The issue is mostly caused by absence of synteny in one (or more) chromosomes. Mostly, this is caused by incorrect strand usage. But as you mentioned that you have corrected the strand, I am not quite sure what else could have caused this.

Could you please share the alignment dotplot for the two genomes? You can use fixchr to generate that.

Also, the file sizes of all the *Out.txt files.

It will also be helpful to have the log file generated by running syri with --log DEBUG parameter.

from syri.

Hi @Pengzw0909. The issue is mostly caused by absence of synteny in one (or more) chromosomes. Mostly, this is caused by incorrect strand usage. But as you mentioned that you have corrected the strand, I am not quite sure what else could have caused this.

Could you please share the alignment dotplot for the two genomes? You can use fixchr to generate that.

Also, the file sizes of all the *Out.txt files.

It will also be helpful to have the log file generated by running syri with --log DEBUG parameter.

Hello,
1.query genome is Lactuca_sativa, about 2.6G, another is Lactuca_virosa. It's too slow. Instead, I use the mummer to get the dotplot png.
cmd：
nucmer LsL46.fa Lviro.fa --maxmatch -c 500 -b 500 -l 100 -t 6 -p LsL46_vs_Lviro && delta-filter -1 -i 90 -l 500 LsL46_vs_Lviro.delta> LsL46_vs_Lviro.filtered.delta
mummerplot -p LsL46_vs_Lviro.all.filter.delta Lviro.all.filter.delta --png

2.the file sizes of all the *Out.txt files：

3.--log DEBUG
syri.log

Thanks you.

from syri.

Syri seems to be exiting because it is not able to find synteny for chromosome 9, which again points to mismatching strands. I cannot recall whether mummerplot internally reverse complements the alignments or not, but if it does then this visualisation would not be helpful. Maybe you try using fixchr/dotplot on only the alignments from Chr9 as that might be fast (you might need to subset the fasta files as well)?

from syri.

Syri seems to be exiting because it is not able to find synteny for chromosome 9, which again points to mismatching strands. I cannot recall whether mummerplot internally reverse complements the alignments or not, but if it does then this visualisation would not be helpful. Maybe you try using fixchr/dotplot on only the alignments from Chr9 as that might be fast (you might need to subset the fasta files as well)?

hello, I get the dotplot of Chr9. There are some structural variation.

1.cmd：
ref=LsL46.Chr09.fasta
qry=Lviro.Chr09.fasta
minimap2 -cx asm20 -t 50 --eqx $ref $qry >minimap2.paf
/share/nas1/pengzw/software/fixchr/bin/dotplot -c minimap2.paf -r LsL46.Chr09.fasta -q Lviro.Chr09.fasta -F P

2.fa：Th file size of Chr09 is too big, about 60Mb. I can't upload.

3.dotplot Chr09：

Thank you for your help~

from syri.

Hi. Indeed it seems that Chr9 needs to be reverse complemented. The two large forward aligned chunks are not linear to each other, rather the currently inverted blue chunks are linear. I think reverse complementing Chr9 (using the other strand) would solve the issue.

from syri.

Hi. Indeed it seems that Chr9 needs to be reverse complemented. The two large forward aligned chunks are not linear to each other, rather the currently inverted blue chunks are linear. I think reverse complementing Chr9 (using the other strand) would solve the issue.

Hi, I do as you say, and the problem is solved. Thank you very much~
the next time, I think changing direction requires a bit of consideration of location.

from syri.