Correupt bowtie2 index file? metaphlan error

Microbial community profiling MetaPhlAn
1

Hi there,

I am trying to run metaphlan both within humann and separately, and am receiving the same error.
Here is a screenshot of the error:

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However, we downloaded the necessary index files from here.
Here is a screenshot of the files we have in the metaphlan database directory we are specifying in our run:

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The “mpa_latest” file lists the newest iteration of the database (i.e., vJan25_*_202503), so I am thinking that this is the problem, but maybe the index files are corrupted? I am just not sure. We are going to recreate a new mpa_latest text file containing the mpa_vJune23_CHOCOPhlAnSGB_202403 index name, but I am not sure what else to do besides redownload the bowtie2 indexes…

Any insight you have regarding this error would be very helpful, thank you!

2

Hi @lfreund
The files seems all to be there and changing the mpa_latest won’t have any effect because that’s only a fallback for when no index is specified, but since you did specify it should try to use the Jun23 version. Can you confirm that you have access to the database folder from the place you are running the metaphlan command? e.g. if you run bowtie2-inspect-l -s /mnt/zarrinpar/Pynchon/Databases/metaphlan/mpa_vJun23_CHOCOPhlAnSGB_202403 does it work?