Maybe consider rpmalloc

[Teemu Nätkinniemi]

The necessary files are in the bwa_reference subfolder. hs37d5.fa in
the command is called a prefix in bwa. The original hs7d5.fa is not
needed.

The command is exactly like I wrote earlier.

./bwa mem -t 10 bwa_reference/hs37d5.fa test_1.fastq.gz
test_2.fastq.gz > test1.sam

Let me know if you have any problems executing the commands.

Teemu

la 3. huhtik. 2021 klo 5.53 Mark Geisert (mark@maxrnd.com) kirjoitti:
>
> Hi Teemu,
> Regarding your test case...
>
> >> Here's a test case:
> >>
> >> bwa_original mem -t 10 bwa_reference/hs37d5.fa ERS4238880_1.fastq > test.sam
> >>
> >> bwa_working mem -t 10 bwa_reference/hs37d5.fa ERS4238880_1.fastq > test.sam
> >>
> >> Files:
> >>
> >> https://drive.google.com/drive/folders/1waICih51f4mHZEyWY1onyEcKqm0kj3Yt?usp=sharing
>
> Could you please put a copy of the file hs37d5.fa into your Google drive folder?
> If that file can be built with the given fastq file and the bwa program, please
> show me how to do that.  A copy+paste from your terminal session would be
> preferable over the video captures you've supplied already, if possible.
> Thank you,
>
> ..mark