From: "Teemu Nätkinniemi" <tnatkinn@gmail.com>
To: Mark Geisert <mark@maxrnd.com>
Cc: "cygwin-developers@cygwin.com" <cygwin-developers@cygwin.com>
Subject: Re: Maybe consider rpmalloc
Date: Sat, 3 Apr 2021 09:48:35 +0300 [thread overview]
Message-ID: <CAEHcbmdYqvfgeq1HUk_ZMC+iL+S-s8uhYBkLSCpWB7o02R471w@mail.gmail.com> (raw)
In-Reply-To: <CAEHcbmc_=scsO5bBc2i3ZqXU_j2o16QHuXhj8616W_ToXRLhWA@mail.gmail.com>
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
next prev parent reply other threads:[~2021-04-03 6:48 UTC|newest]
Thread overview: 17+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-09-25 6:01 Cygwin malloc tune-up status Mark Geisert
2020-09-27 16:54 ` Johannes Schindelin
2020-09-29 2:22 ` Mark Geisert
2021-04-01 9:19 ` Teemu Nätkinniemi
2021-04-02 5:45 ` Maybe consider rpmalloc -- Was: " Mark Geisert
2021-04-03 2:53 ` Maybe consider rpmalloc Mark Geisert
2021-04-03 6:46 ` Teemu Nätkinniemi
2021-04-03 6:48 ` Teemu Nätkinniemi [this message]
2021-04-11 9:28 ` Mark Geisert
2021-04-12 8:48 ` Teemu Nätkinniemi
2021-04-13 8:24 ` Mark Geisert
2021-04-13 13:05 ` Teemu Nätkinniemi
2021-04-14 8:19 ` Mark Geisert
2021-04-14 18:36 ` Teemu Nätkinniemi
2021-04-14 18:53 ` Jon Turney
2021-04-19 5:16 ` Mark Geisert
2021-04-20 19:34 ` Jon Turney
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