empty output of chroder

[kendaida]

Hi, thank you for developing cool tool.
I know that there are several posts about this but I cannot solve my problem.

I am trying to use denovo assembly with scaffold level and reference genome, using pseudo genome assembly,
It runs but the output of the chroder "out_ref.fasta" was an empty file.
"output.qry.fasta" seems to be good including the same number of Chromosome as the reference genome.

Tried syri with "out_ref.fasta" or the reference fasta, it got the error "Chromosomes IDs do not match."

Thanks for your help.

[mnshgl0110]

Hi. Could you please share the chromosome IDs in the reference and the chroder_qry genome? If the number of chromosomes are same then this error should not happen. Also, please run syri with --log DEBUG and share the log file.

Additionally, if there is a chromosome level reference genome available, then you can also try using ragtag as that generates better pseudo-chromosomes then chroder.

[kendaida]

Thanks for your help.

I made a denovo assembly for human genome chr6.
And using hg38 as a reference, extracting the chr6 by samtools.

The output from chroder output.qry.fasta includes

chr6

And the reference includes

chr6

the log file for syri
2023-03-01 23:27:54,823 - Reading Coords - DEBUG - syri:135 - T
2023-03-01 23:27:54,824 - Reading Coords - INFO - syri:135 - Reading input from .tsv file
2023-03-01 23:27:54,841 - Reading Coords - WARNING - syri:135 - Chromosomes IDs do not match.
2023-03-01 23:27:54,841 - Reading Coords - ERROR - syri:135 - Unequal number of chromosomes in the genomes. Exiting

I'll try ragtag!

[mnshgl0110]

Does your reference has only chr6 or other chromosomes as well? Make sure that the reference and query genomes have same number of chromosomes.

[kendaida]

Thanks for your help.

The reference only includes chr6.

My code is like below.

GRCh38_chr6.fa includes only "chr6".
$A_fa is the assembled fasta for chrmosome 6 by Shasta

nucmer --maxmatch -c 500 -b 500 -l 100  GRCh38_chr6.fa $A_fa
delta-filter -m -i 90 -l 100 out.delta > out_filtered.delta
show-coords -THrd out_filtered.delta > out_filtered.coords
chroder -o output out_filtered.coords $BASE_DIR/GRCh38_chr6.fa $A_fa

the output of chroder output.ref.fasta is empty.
So used the reference for syri.

Confirmed input of syri has same chromosome.

grep ">" GRCh38_chr6.fa
>chr6

grep ">" output.qry.fasta 
>chr6

Then run syri.
However, the error message below are printed.

syri -c out_filtered.coords -d out_filtered.delta -r GRCh38_chr6.fa -q output.qry.fasta

2023-03-02 09:58:17,701 - Reading Coords - INFO - syri:135 - Reading input from .tsv file
2023-03-02 09:58:17,721 - Reading Coords - WARNING - syri:135 - Chromosomes IDs do not match.
2023-03-02 09:58:17,722 - Reading Coords - ERROR - syri:135 - Unequal number of chromosomes in the genomes. Exiting

I also tried ragtag but it does not solve the situation.

[mnshgl0110]

If I understand correctly, in the following command:
syri -c out_filtered.coords -d out_filtered.delta -r GRCh38_chr6.fa -q output.qry.fasta
you are using the alignments generated between GRCh38_chr6.fa and A_fa.
For comparing GRCh38_chr6.fa and output.qry.fasta, you need to get genome alignment between them and use those with syri.

[kendaida]

Oh thank you!
I re-run mummer with the two fasta file and finally got the output of plotsr!

Is it usual to get empty output of reference fasta ("output.ref.fasta") from chroder if I use the chromosome level assembly as an reference?