missing sequence counts in summary file

[mnshgl0110]

Hi @mnshgl0110 , In my summary file, structural annotations have values only, but in sequence annotations, all counts are showing 0 only. like attached below

Structural annotations

Variation_type Count Length_ref Length_qry

Syntenic regions 7188 2535240608 2528221404 Inversions 283 2464865 2439444 Translocations 8547 69687524 66748895 Duplications (reference) 955 6718295 - Duplications (query) 6400 - 26763094 Not aligned (reference) 13165 82618600 - Not aligned (query) 21911 - 80606870

Sequence annotations

Variation_type Count Length_ref Length_qry

SNPs 0 0 0 Insertions 0 - 0 Deletions 0 0 - Copygains 0 - 0 Copylosses 0 0 - Highly diverged 0 0 0 Tandem repeats 0 0 0

the command that I used was: syri -c out.filtered.coords -d out.filtered.delta -r reference.fasta -q query.fasta -f --nc 50 --prefix new --all

Thank you

Originally posted by @sahu-git in https://github.com/schneebergerlab/syri/issues/144#issuecomment-1157556576

[mnshgl0110]

@sahu-git for my runs it is working. Maybe try reinstalling syri and running it again in an empty folder. Also, check whether there are SNPs or indels in the syri.out file.

[ASBioinfo]

hi thanks for your quick response @mnshgl0110 ,

snp.txt file was generated as an intermediate file with SNPs but in syri.out file no SNPs or indels are present. I tried with the reinstallation, still it not working

Thank you

[mnshgl0110]

Could you please run syri with --log debug and share the syri.log file?

[ASBioinfo]

Thanx, I attached the log file below syri.log

[mnshgl0110]

SNPs/indels are identified and processed for writing as clear by this log line (snps = ShV): All annotation count. SR anno: 1412 SV anno: 102 ShV anno: 117903 notal anno: 403. But there is no hint on what could be going wrong.

Could you share a minimal example for me to check (input genome files, alignments, and the commands)?

[ASBioinfo]

I attached files below (I run on the example file) out.filtered.delta.gz reference.fasta.gz newsyri.summary.gz out.filtered.coords.gz query.fasta.gz

[mnshgl0110]

I ran syri using these files and the command that you mentioned above and got complete newsyri.summary.gz file.

So, I still have no idea why it is not working for you.

Did you install syri from bioconda or github, and if github then you which branch?

[ASBioinfo]

I get the repository by git clone from the GitHub master branch. ok, I will try to recheck again by bioconda.

thank you