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 09:46:39 +0300 [thread overview]
Message-ID: <CAEHcbmc_=scsO5bBc2i3ZqXU_j2o16QHuXhj8616W_ToXRLhWA@mail.gmail.com> (raw)
In-Reply-To: <6f68b10b-7fe5-4378-afb9-9001de084edf@maxrnd.com>
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 6:46 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 [this message]
2021-04-03 6:48 ` Teemu Nätkinniemi
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
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to='CAEHcbmc_=scsO5bBc2i3ZqXU_j2o16QHuXhj8616W_ToXRLhWA@mail.gmail.com' \
--to=tnatkinn@gmail.com \
--cc=cygwin-developers@cygwin.com \
--cc=mark@maxrnd.com \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).