Vasimuddin Md comments

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                                            Vasimuddin Md

Memory Issue

Thanks for the feedback. How frequently bwa-mem2 is failing (% of datasets it is failing on)? Also, do you know how much memory bwa-mem takes for the same datasets?

Specific use case

you can do it manually: extract the sequence of interest and run indexing and mapping.

Segmentation fault with bwa-mem2 mem

Sorry about the delay. We are looking into it and should get back to you very soon.

Segmentation fault with bwa-mem2 mem

Sorry for getting back so late, will it be possible to re-share the file. They are inaccessible.

no alignments with MiSeq paired-end reads

Could you share some data (reads) with which I can reproduce the issue?

no alignments with MiSeq paired-end reads

The link is broken now. Could you re-share the data, thanks.

no alignments with MiSeq paired-end reads

Thanks !!

bwamem2 as a library and linking to own project

Sorry about the delay, we are working on it, will try to incorporate the feature in the next release.

Range violation

@christopher-schroeder are you still facing the problem? What is the memory capacity of this system? can you try and check with smaller number of threads?

Range violation

The available memory is sufficient to run mem2. You can start with 16 threads. The log shows that it is hanged in the seeding stage. Also, you can try the...