Your message dated Mon, 12 Feb 2024 04:00:11 +0000 with message-id <E1rZNUJ-00A5MX-3v@fasolo.debian.org> and subject line Bug#962484: fixed in deblur 1.1.1-1 has caused the Debian Bug report #962484, regarding ITP: deblur -- deconvolution for Illumina amplicon sequencing to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 962484: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962484 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
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- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: deblur -- deconvolution for Illumina amplicon sequencing
- From: Steffen Moeller <moeller@debian.org>
- Date: Mon, 08 Jun 2020 19:14:49 +0200
- Message-id: <159163648997.129526.16028696690341896029.reportbug@steffen-laptop-debian.ffoh>
Package: wnpp Severity: wishlist Subject: ITP: deblur -- deconvolution for Illumina amplicon sequencing Package: wnpp Owner: Steffen Moeller <moeller@debian.org> Severity: wishlist * Package name : deblur Version : 1.1.0 Upstream Author : , Deblur development team * URL : https://github.com/biocore/deblur * License : BSD-3 Programming Lang: Python Description : deconvolution for Illumina amplicon sequencing Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles. The authors recommend using Deblur via the QIIME2 plugin q2-deblur. Examples of its use can be found within the plugin itself. However, Deblur itself does not depend on QIIME2. . The input to Deblur workflow is a directory of FASTA or FASTQ files (1 per sample) or a single demultiplexed FASTA or FASTQ file. These files can be gzip'd. The output directory will contain three BIOM tables in which the observation IDs are the Deblurred sequences. The outputs are contingent on the reference databases used and a more focused discussion on them is in the subsequent README section titled "Positive and Negative Filtering." The output files are as follows: . * reference-hit.biom : contains only Deblurred reads matching the positive filtering database. By default, a reference composed of 16S sequences is used, and this resulting table will contain only those reads which recruit at a coarse level to it will be retained. Reads are also filtered against the negative reference, which by default will remove any read which appears to be PhiX or adapter. . * reference-hit.seqs.fa : a fasta file containing all the sequences in reference-hit.biom . * reference-non-hit.biom : contains only Deblurred reads that did not align to the positive filtering database. Negative filtering is also appied to this table, so by default, PhiX and adapter are removed. . * reference-non-hit.seqs.fa : a fasta file containing all the sequences in reference-non-hit.biom . * all.biom : contains all Deblurred reads. This file represents the union of the "reference-hit.biom" and "reference-non-hit.biom" tables. . * all.seqs.fa : a fasta file containing all the sequences in all.biom . Deblur uses two types of filtering on the sequences: . * Negative mode - removes known artifact sequences (i.e. sequences aligning to PhiX or Adapter with >=95% identity and coverage). . * Positive mode - keeps only sequences similar to a reference database (by default known 16S sequences). SortMeRNA is used, and any sequence with an e-value <= 10 is retained. Deblur also outputs a BIOM table without this positive filtering step (named all.biom). . The FASTA files for both of these filtering steps can be supplied via the --neg-ref-fp and --pos-ref-fp options. By default, the negative database is composed of PhiX and adapter sequence and the positive database of known 16S sequences. . Deblur uses negative mode filtering to remove known artifact (i.e. PhiX and Adapter sequences) prior to denoising. The output of Deblur contains three files: all.biom, which includes all sOTUs, reference-hit.biom, which contains the output of positive filtering of the sOTUs (default only sOTUs similar to 16S sequences), and reference-non-hit.biom, which contains only sOTUs failing the positive filtering (default only non-16S sOTUs). Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/deblur
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- To: 962484-close@bugs.debian.org
- Subject: Bug#962484: fixed in deblur 1.1.1-1
- From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
- Date: Mon, 12 Feb 2024 04:00:11 +0000
- Message-id: <E1rZNUJ-00A5MX-3v@fasolo.debian.org>
- Reply-to: Andreas Tille <tille@debian.org>
Source: deblur Source-Version: 1.1.1-1 Done: Andreas Tille <tille@debian.org> We believe that the bug you reported is fixed in the latest version of deblur, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 962484@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <tille@debian.org> (supplier of updated deblur package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 30 Jan 2024 20:14:25 +0100 Source: deblur Binary: deblur Architecture: source all Version: 1.1.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Andreas Tille <tille@debian.org> Description: deblur - deconvolution for Illumina amplicon sequencing Closes: 962484 Changes: deblur (1.1.1-1) unstable; urgency=medium . * Team upload. * Initial release (Closes: #962484) Checksums-Sha1: e191cccef16e0318e6b3eab08ad89d1ba3175d87 2072 deblur_1.1.1-1.dsc e6e86817af379b29fbed698573f3463d154a16bf 3901272 deblur_1.1.1.orig.tar.gz 5e864743071faaea76c470f47770975f1dedf783 3500 deblur_1.1.1-1.debian.tar.xz ea73d57efeeb86d7e74671d836005443195ec03f 1730588 deblur_1.1.1-1_all.deb 95181a891173a7a69739fb0815ef196c1a5c247e 10805 deblur_1.1.1-1_amd64.buildinfo Checksums-Sha256: bdffd98da68882025edce361cefd924137746b3cc963b93d32220c4977087b3f 2072 deblur_1.1.1-1.dsc a4d60bde48de1619300a20e689cf80f367c45649f73ce7d196fcfe2db70d3d40 3901272 deblur_1.1.1.orig.tar.gz 247267fb427ff218c5e848f11534be80312328595d369a4ae1090635c27ed6bd 3500 deblur_1.1.1-1.debian.tar.xz fc0f2bfc49ff3ce656f224ff8a433d792c8401c2656a76358d0ba9bd63b9a788 1730588 deblur_1.1.1-1_all.deb af9f7f4595cbdcd105800ac70558a04983d85280c97085ed3ce558c7b1e155ee 10805 deblur_1.1.1-1_amd64.buildinfo Files: c0fcacd7d098b36ca3f2d6d5f0d8b3cf 2072 science optional deblur_1.1.1-1.dsc 38ee00ccde82293c5f122ee36dc4bf25 3901272 science optional deblur_1.1.1.orig.tar.gz 0bbee26119526a8a910b192360aba89b 3500 science optional deblur_1.1.1-1.debian.tar.xz e52a35f10f32a5dca7353347959f467a 1730588 science optional deblur_1.1.1-1_all.deb af456e0609ab424ef11b5ec139b7d792 10805 science optional deblur_1.1.1-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW79F4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEXfQ/9GObOJxoaEibbC8QH3i7ZTkOAM+CR7P5T 02cm/qRXVMtl1XK5AwN+OaCrpIVLagQN2TYsGqb8i7Ts0Ti/9WSaz9lx9F6eaKaK 8T7AwWvwd24K4iJxT27eL+gTxxqsiiRIiimV6zWeBzRTh/udFYofqfiSuddRKcOW QO4kOVH/PzSmjKvD43TRvFY87yqOm6igRLzr/8aImkQZ+yAixcDuR1nmFnjzg4Y9 ONWT0tTON/7YDH2ycpMAzioBN23NIj8fhegtMAvg8nBP+W+XUUR/4Q29OFz8QjED TMMPg5zYvg/9o9lUWjtLmB0Tx1pJQrbt7DYWY/dyCCti21ZhH9Bx72dFUYcdeudu N9aJBCy9/LxZ0+2/FmeT5B7EeFaqF1h20MqAyLubugsirCe3YbjrDkfmELQJEsZB gYeR5vtfqgSK+Yok4A7bW6MMMm3s/yncaiWm5zlBJjAlByM+M/Fq2R26/5iA9e1R X2dI4KPW0Mvxjh/m+orkdwF8WOan6P9UU/v4c5bBlxJUQXAXD2uOHB9ToxiM+Hb/ R5Twr0+7UYB84wFo6tT6B9coGNATb0sHuTiMJrvYi9Tm7d8/RXhp5mszVR5W9iEl Ub+vcRR0BWop9EnFlQgX1hRL+qjZehGAs/VS2H0ettgKBZWMIDQBthYT531V+gJ/ Ie+xCJt01h4= =lpj6 -----END PGP SIGNATURE-----Attachment: pgptiFTWUf0U2.pgp
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