The file https://huttenhower.sph.harvard.edu/kneadData_databases/Homo_sapiens_hg39_T2T_Bowtie2_v0.1.tar.gz uncompresses to a subdirectory called bowtie2-index. This is a different behavior than previous and also different from other kneaddata bowtie indexes. The result is that kneaddata doesn’t run without manually moving the bt2 index files up one level in the filesystem or specifying a different database directory for the kneaddata run from the directory specified in the kneaddata_databases download.
Hi @seandavi ,
Thank you for testing out the new release v0.12.3. I will get the new database structure consistent with the other older database and let you know here. This should be quick and easy.
Regards,
Sagun
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Hi @seandavi ,
Just a heads up that we have now updated the same directory structure for the new T2T bowtie2 DB as well. Please feel free to test it out and let me know if you see any other issues.
Regards,
Sagun