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Diamond blast running in a loop

Hi ! I am using diamond blast (blastx) to align nanopore reads against NR database. The process runs fine until the last bin but suddenly gets in a loop and restarts the complete process again. It works fine on 1000 reads but dowmsampling to 1 million also sows same issue without throwing any error.

Any help appreciated. Thank you.

nanopore blast diamond
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written by bioinfo_ga • bioinfo_ga

The process runs fine until the last bin but suddenly gets in a loop and restarts the complete process again.

So the process starts over? Have you checked to the logs to see if there is any useful info there? How many threads are you running?

Author of DIAMOND notes the following for the memory requirements:

The memory needed depends on the options -b and -c, it is roughly 20*b/c. 

--block-size (-b)        sequence block size in billions of letters (default=2.0)
--index-chunks (-c)      number of chunks for index processing (default=4)

There are a couple of threads on this by author of DIAMOND that may be useful:
https://github.com/bbuchfink/diamond/issues/397
https://github.com/bbuchfink/diamond/issues/629

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written by GenoMax GenoMax

okay will try with the new parameters .

Thank you

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written by bioinfo_ga • bioinfo_ga

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