Issue with StrainScan_build during database construction

liaoherui / StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01615-w

MIT License

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Issue with StrainScan_build during database construction #18

Open BZhao95 opened 5 months ago

BZhao95 commented 5 months ago

Hi,

I am encountering a problem with StrainScan during the construction of a Vibrio parahaemolyticus database. The process has been stuck at the "merge genomes" and "run Sibeliaz" (as shown in the screenshot atttached). This has been the case for several weeks, regardless of the number of genomes processed.

I have updated the StrainScan to the latest version. Could you please provide some guidance or a solution to overcome this problem? Any help would be greatly appreciated.

Thank you.

Best. Bing

liaoherui commented 5 months ago

Hi, thanks for using StrainScan!

It appears that the issue you're experiencing is related to the usage of the "sibeliaz" (https://github.com/medvedevgroup/SibeliaZ) tool, which is utilized by StrainScan. To troubleshoot this, I recommend running the command manually to see if it works. You can try executing "sibeliaz -n -m 100 -k 15 -a 750 -o ....." and observe the results. If the problem persists, please feel free to send your input genomes to me via email (heruiliao2-c@my.cityu.edu.hk) or any other convenient method for further testing. Thanks!