Maybe consider rpmalloc

[Teemu Nätkinniemi]

Sorry, hurt my back yesterday and looks like I am not thinking clearly.

./bwa mem -t 10 bwa_reference/hs37d5.fa ERS4238880_1.fastq > test1.sam

la 3. huhtik. 2021 klo 9.46 Teemu Nätkinniemi (tnatkinn@gmail.com) kirjoitti:
>
> 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