From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mail-ed1-x534.google.com (mail-ed1-x534.google.com [IPv6:2a00:1450:4864:20::534]) by sourceware.org (Postfix) with ESMTPS id E3D5A385781B for ; Sat, 3 Apr 2021 06:46:51 +0000 (GMT) DMARC-Filter: OpenDMARC Filter v1.3.2 sourceware.org E3D5A385781B Received: by mail-ed1-x534.google.com with SMTP id x21so7361290eds.4 for ; Fri, 02 Apr 2021 23:46:51 -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; bh=53c8seYz1JEMAT0W0Y1nylsq4y4xRVVaOWJK6iVB9lk=; b=S9OdIS2qwJR34EESl2RHEuyGK0S0ugAZhpH2KH9Z/kaYw04eV07X/ZmOiP9W7LomNh GL5CYQKOczXsqrJGnTWFo1/wS3gODLXvP1C1mobPrjVlV1va6yiPby0/IZNbyGEwfTmV uOLJt84m5+oYeGy+zx40dAY6WVW1OJTtyIPKOBN14yhj1A+D5Bn8a1eSYA+LUxbUyibN xwfjm80pw3zX0glUYJ8xUWUG3USgtgxIEl8zAuV7QuO+SBJahbsr22oJZC+WklxWlrBo VvGFbfw6Yu7qxMeg+UrHqveJg5XFr1sF4ZOiBo8Sg8AxXgrt2hlTn9jEnv0exS1I9wZf h9vg== X-Gm-Message-State: AOAM5323zNLYhSu8ZuJT3mFgTVWWk4he1t6fVRIwu+Rv7i4GGeNIKAki pqRHun5QVdn2cWqmCLUwFe/a6zzSRlJf2iP8AxR+DsWqEic= X-Google-Smtp-Source: ABdhPJwmax2qFc+Jl5Z5waDSy5zt4/dlKbilsiOiswc0DkngWy3fTfu6EMjvzXB5mLAYTxy9vSXyspodAvsAifYo9YI= X-Received: by 2002:aa7:ca12:: with SMTP id y18mr3906295eds.41.1617432410900; Fri, 02 Apr 2021 23:46:50 -0700 (PDT) MIME-Version: 1.0 References: <067987e2-e958-b56c-efea-25d827568453@maxrnd.com> <6f68b10b-7fe5-4378-afb9-9001de084edf@maxrnd.com> In-Reply-To: <6f68b10b-7fe5-4378-afb9-9001de084edf@maxrnd.com> From: =?UTF-8?Q?Teemu_N=C3=A4tkinniemi?= Date: Sat, 3 Apr 2021 09:46:39 +0300 Message-ID: Subject: Re: Maybe consider rpmalloc To: Mark Geisert Cc: "cygwin-developers@cygwin.com" Content-Type: text/plain; charset="UTF-8" X-Spam-Status: No, score=-1.8 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 06:46:53 -0000 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