can not output Syri.out

[aaannaw]

Hello,Professor I am running the Syri with my two genome according to the example.sh:

nucmer -l 40 -c 200 -b 50 -p out A.fasta B.fasta -t 10(note: because of the parameter --maxmatch costs too much time,so I delete it)
delta-filter -m -i 90 -l 100 out.delta  > out.filtered.delta
show-coords -THrd  out.filtered.delta  >out.coords
python3 ~/miniconda3/envs/syri_env/bin/syri -c out.coords -d out.filtered.delta -r A..fasta -q B.fasta -s ~/miniconda3/envs/mummer4/bin/show-snps --nc 10

The results is *dupOut.txt ,*invDupOut.txt,*invOut.txt by chromosomelike the following the picture and there is no dupOut.txt ,invDupOut.txt,*invOut.txt of several chromosomes. At the same time, I can not produce the syri.out either by chr or whole genome like the example. I have successfully run the example. Could you give me any suggestions? Thanks so much! syri.log

[mnshgl0110]

There is not anything obviously wrong in the log file. Are there any error messages?

[aaannaw]

The task I submit by SLURM "python3 ~/miniconda3/envs/syri_env/bin/syri -c out.coords -d out.filtered.delta -r A..fasta -q B.fasta -s ~/miniconda3/envs/mummer4/bin/show-snps --nc 10"is still ruuning, but it has produced nothing for two hours after poroducing the above files. In my submit task, the .err file storing standard error has nothing and the .out file storing standard out has the message:

Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - WARNING - Matching them automatically. For each reference genome, most similar query genome will be selected. Check mapids.txt for mapping used

I am not sure if it it the normal. I have tried several times, the above files occurs for a short time, and then the task seems to be sleeping, nothing to produce.

[aaannaw]

Before running the example pipline, I slightly deal with my two chromosome level genome by chroder. Because my chromosome genome level has different chromosome numbers. So I use chroder to get the homologous genome of equal numer of chromosomes: chroder -o out -F T A.B.coords A.only.chr.fasta B.only.chr..fasta The output out.qry.fasta is semmed as the homologus of ref genome A.only.chr.fasta, Then I run the pipline above. Maybe the use of chroder influence the results?

[mnshgl0110]

For large, highly repetitive genomes, it can take some time for jobs to finish. It is expected and not an error.