From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mail-ed1-x531.google.com (mail-ed1-x531.google.com [IPv6:2a00:1450:4864:20::531]) by sourceware.org (Postfix) with ESMTPS id 78947385781B for ; Sat, 3 Apr 2021 06:48:47 +0000 (GMT) DMARC-Filter: OpenDMARC Filter v1.3.2 sourceware.org 78947385781B Received: by mail-ed1-x531.google.com with SMTP id z1so7347671edb.8 for ; Fri, 02 Apr 2021 23:48:47 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=r5NuHVH9pJdGHHzKScrlfnbH0W1TJlEd8hNs1S4AMlY=; b=cd4lvrGsXlSMY7QwnAVfbA3lyIMle9qfUpGp5tUWvarxZaNatVySAlBO5Uduukc9Jm dbRY3GGc1WAdMcp8iAk1XtN63PtASkSvlanXKzNUWtlgTBpZs8G4uQJ7Jy4ArRKZvcO8 uwVvQ2PNojCg/8n44eFCRKf0iw4kLNViChDaveh3zx+a8nmZuqVYysaEklQMnh8J3k91 ZbO1/oEKn4lBvGipJQ6d2p9+HNuqPBACKOLKJaHWTBr7byAYGDO5J4GGXvvW9VBMrw77 buTkKUXHQmv/ZPVpZdP3gbK5vl0Y3vutYg3Nbt+RtXV9yPXyKTOXhjKbfKq83pONhI+U sbLg== X-Gm-Message-State: AOAM532Rs2qRSOZM0rdjaYa6Fn0pZ2SLVA74Jp2muHDmGczXuvrpBOIH QQw/llK+uAk4bZl/O9NCJV9uETUc2bSXYqu35JXo9J406ws= X-Google-Smtp-Source: ABdhPJz/5ceiONS+oCpb3LJNxUtPJ9Y5k/bNXiAe+PH+lQjr8r4wh/6AuiCV2fy0B8YtRv4jncVPys54USJqHBhXWPE= X-Received: by 2002:a05:6402:22bb:: with SMTP id cx27mr19290636edb.148.1617432526618; Fri, 02 Apr 2021 23:48:46 -0700 (PDT) MIME-Version: 1.0 References: <067987e2-e958-b56c-efea-25d827568453@maxrnd.com> <6f68b10b-7fe5-4378-afb9-9001de084edf@maxrnd.com> In-Reply-To: From: =?UTF-8?Q?Teemu_N=C3=A4tkinniemi?= Date: Sat, 3 Apr 2021 09:48:35 +0300 Message-ID: Subject: Re: Maybe consider rpmalloc To: Mark Geisert Cc: "cygwin-developers@cygwin.com" Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Status: No, score=-1.4 required=5.0 tests=BAYES_00, DKIM_SIGNED, DKIM_VALID, DKIM_VALID_AU, DKIM_VALID_EF, FREEMAIL_FROM, RCVD_IN_DNSWL_NONE, SPF_HELO_NONE, SPF_PASS, TXREP autolearn=ham autolearn_force=no version=3.4.2 X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on server2.sourceware.org X-BeenThere: cygwin-developers@cygwin.com X-Mailman-Version: 2.1.29 Precedence: list List-Id: Cygwin core component developers mailing list List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 03 Apr 2021 06:48:48 -0000 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 N=C3=A4tkinniemi (tnatkinn@gmail.com) kir= joitti: > > 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 > t= est.sam > > >> > > >> Files: > > >> > > >> https://drive.google.com/drive/folders/1waICih51f4mHZEyWY1onyEcKqm0k= j3Yt?usp=3Dsharing > > > > Could you please put a copy of the file hs37d5.fa into your Google driv= e 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