[From nobody Thu Jul 9 19:03:06 2026 Received: (at submit) by bugs.debian.org; 2 Jul 2026 17:01:29 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-122.5 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FROMDEVELOPER,HAS_PACKAGE, SPF_HELO_NONE,SPF_PASS,USER_IN_DKIM_WELCOMELIST,XMAILER_REPORTBUG autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 32; hammy, 150; neutral, 198; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <wrar@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:49568) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <wrar@debian.org>) id 1wfKn3-00EsjZ-1v for submit@bugs.debian.org; Thu, 02 Jul 2026 17:01:29 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Date:Message-ID:Subject:To:From: Content-Transfer-Encoding:MIME-Version:Content-Type:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=yz1fXW3nW5Oi6pa+2I+yBCodnmfLweWM1xH90Tt9juQ=; b=fc3xgJ1HNY9b7uf0ov+r1Njdv3 ywJF4ENFSByU/xxV+kX0bg7/2U9J6q0lnHDCqyNPvth325nrzuP76zSh5BQt8ig5fhuaB+5JyskPn WklArzqBnidu800x99Fq0Jjv0/NzPU7+sNYFTuetOb4Taj2AAuhl/mBy8ur8wkuyjwUmIxS4dmDR4 bY6nw30pP4lVnSpTYanhgDREY6pL0X4x/fvwuoryH/JW4WMUQFy8qndoqRoDrBvBOpADQaysGDS8D UAF0Ohpt3tMSMRz4XPJdTPklYoNmvgXu+8T6uAAkX7o51TaGzoZagC9Y7ATXZdLoxkzXL+z0UUA1b 2o6j3AJA==; Received: from authenticated-user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <wrar@debian.org>) id 1wfKn2-008ltv-0F; Thu, 02 Jul 2026 17:01:28 +0000 Received: from [188.226.55.174] (helo=belkar.localdomain) by durkon.wrar.name with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.99.4) (envelope-from <wrar@debian.org>) id 1wfKn1-00000008FwZ-1LXC; Thu, 02 Jul 2026 19:01:27 +0200 Received: by belkar.localdomain (Postfix, from userid 1000) id 590FB6A39203; Thu, 02 Jul 2026 22:01:26 +0500 (+05) Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: Andrey Rakhmatullin <wrar@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: iva: Autopkgtests fail: File "hiv_pcr_primers.fa" not found. Message-ID: <178301168634.1043186.7404548943706944970.reportbug@belkar.wrar.name> X-Mailer: reportbug 13.2.0+nmu1 Date: Thu, 02 Jul 2026 22:01:26 +0500 X-Debian-User: wrar Delivered-To: submit@bugs.debian.org Package: iva Version: 1.0.11+ds-6 Severity: serious The following command failed with exit code 1 /usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out The output was: Error! File "hiv_pcr_primers.fa" not found. Cannot continue Traceback (most recent call last): File "/usr/bin/iva", line 184, in <module> p1.start() ~~~~~~~~^^ File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) ~~~~~~~~~~~^^^^^^ File "/usr/lib/python3.14/multiprocessing/context.py", line 230, in _Popen return _default_context.get_context().Process._Popen(process_obj) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/context.py", line 306, in _Popen return Popen(process_obj) File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ super().__init__(process_obj) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) ~~~~~~~~~~~~^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in _launch self.sentinel, w = forkserver.connect_to_new_process(self._fds) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in connect_to_new_process connection.answer_challenge( ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ wrapped_client, self._forkserver_authkey) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/connection.py", line 995, in answer_challenge message = connection.recv_bytes(256) # reject large message File "/usr/lib/python3.14/multiprocessing/connection.py", line 226, in recv_bytes buf = self._recv_bytes(maxlength) File "/usr/lib/python3.14/multiprocessing/connection.py", line 451, in _recv_bytes buf = self._recv(4) File "/usr/lib/python3.14/multiprocessing/connection.py", line 416, in _recv chunk = read(handle, to_read) ConnectionResetError: [Errno 104] Connection reset by peer -- System Information: Debian Release: forky/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'), (101, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 7.0.13+deb14-amd64 (SMP w/16 CPU threads; PREEMPT) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=ru_RU.UTF-8, LC_CTYPE=ru_RU.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages iva depends on: ii default-jre-headless 2:1.25-77 pn fastaq <none> pn kmc <none> pn mummer <none> ii perl 5.40.1-8 ii python3 3.13.9-3+b1 pn python3-networkx <none> ii python3-numpy 1:2.4.6+ds-2 ii python3-packaging 26.2-2 pn python3-pysam <none> pn samtools <none> pn smalt <none> Versions of packages iva recommends: pn bioperl <none> pn r-base-core <none> pn trimmomatic <none> iva suggests no packages. ]