bbuchfink/diamond issues and pull requests

#835 - Testsuite crashes with "Bus error" on sparc64 due to bad alignment

Issue - State: open - Opened by glaubitz about 2 months ago - 4 comments

#833 - DIAMOND index is refusing to build; error: Writing sequences... /cm/local/apps/slurm/var/spool/job16162007/slurm_script: line 16: 3788602 Killed ./diamond makedb --in nr.gz -d nr slurmstepd: error: Detected 1 oom_kill event in StepId=16162007.batch. Some of the step tasks have been OOM Killed.

Issue - State: closed - Opened by lyisrae1 2 months ago

#832 - Minimum query length in diamond blastp

Issue - State: open - Opened by bucongfan 2 months ago - 1 comment

#831 - Change FDIV to FMUL

Pull Request - State: closed - Opened by heshpdx 2 months ago

#830 - 希望支持对非生物数据的支持

Issue - State: open - Opened by DengYongjiuDengYongjiu 3 months ago

#829 - Optimising the speed of DIAMOND based on the size of input queries (and other)

Issue - State: open - Opened by charlesfoster 3 months ago

#828 - Fix for uninitialized variable

Pull Request - State: closed - Opened by heshpdx 3 months ago

#827 - ERROR [diamond_search()]

Issue - State: open - Opened by hysong0921 3 months ago

#826 - Unrecognized sequence character in BLAST database

Issue - State: open - Opened by anearman 3 months ago

#825 - option --memory-limit raises error

Issue - State: open - Opened by h836472 4 months ago

#824 - Using MAGs as input

Issue - State: open - Opened by chrissy005 4 months ago

#823 - "Error: Array size overflow" when using Diamond on large custom database

Issue - State: open - Opened by CaroleBelliardo 4 months ago

#822 - Documentation for realign is not updated

Issue - State: open - Opened by dvillarreal4868 4 months ago

#821 - "Tabulator character in sequence title" warning

Issue - State: open - Opened by Somebodyatthdoor 4 months ago

#820 - output parameter prevents diamond realign workflow

Issue - State: open - Opened by tag92-CornellUniv 4 months ago

#819 - Hit not found for certain queries with custom 1/-1 matrix

Issue - State: open - Opened by tanhevg 5 months ago - 1 comment

#818 - consistency of option "--outfmt 6 qseq sseq" with blastp

Pull Request - State: open - Opened by kad-ecoli 5 months ago

#817 - tmpdir issue

Issue - State: open - Opened by mintonrl 5 months ago

#816 - paired-end diamond with local database

Issue - State: open - Opened by 2061574124 5 months ago

#815 - segmentation fault

Issue - State: open - Opened by juliayork 5 months ago

#814 - --global-ranking, impact and when to set lower?

Issue - State: open - Opened by fpusan 5 months ago

#813 - Conda/bioconda install - packages not found error

Issue - State: open - Opened by ryan-boobybiome 5 months ago - 1 comment

#812 - Cannot include both --query_cover and --subject_cover in my search.

Issue - State: open - Opened by KPapac 5 months ago

#811 - Diamond with database of small kmers

Issue - State: open - Opened by raeshrode 6 months ago

#810 - Request: pre-built databases for download

Issue - State: open - Opened by bheimbu 6 months ago

#809 - Error: Error opening temporary file 24/diamond-tmp-YA0Xiz

Issue - State: open - Opened by JipengLuo 6 months ago

#808 - Linking CXX executable diamond fails during make

Issue - State: open - Opened by Monkjj 6 months ago - 1 comment

#807 - singular version of staxids command?

Issue - State: open - Opened by ewaltari 6 months ago - 1 comment

#806 - Error running tutorial : "Computing alignments... Illegal instruction: 4" (MACOS)

Issue - State: open - Opened by rberlemont 6 months ago

#805 - Blast database formatted with prepdb does not support taxonomic information

Issue - State: open - Opened by cedricblais 6 months ago - 3 comments

#804 - Use custom score matrix error？

Issue - State: open - Opened by liufuyan2016 6 months ago - 1 comment

#803 - Error: Invalid parameter count for option '--tmpdir'

Issue - State: open - Opened by lhxaurora 6 months ago - 2 comments

#802 - Is there an option like blastp to set word size for short sequences?

Issue - State: open - Opened by ZhangBioLab 7 months ago - 1 comment

#801 - When running diamond blastp in multiprocessing mode, some processes hang or segfault non deterministically.

Issue - State: open - Opened by beazerj 8 months ago - 1 comment

#800 - Could not find diamond in dependencies/ folder.

Issue - State: closed - Opened by karthickbrlab 8 months ago

#799 - trying to use diamon on macos

Issue - State: open - Opened by keecarter 8 months ago - 1 comment

#798 - `view qseq` uses letters `ARND` instead of `ACTG`

Issue - State: open - Opened by imLew 8 months ago - 2 comments

#797 - Feature request: PSSM output and input

Issue - State: open - Opened by DanBuchan 8 months ago - 2 comments

#796 - Diamond view throws segmentation fault (core dumped) error

Issue - State: open - Opened by SaimMomin12 8 months ago - 1 comment

#795 - resident size (66266557647) exceeds memory limit

Issue - State: closed - Opened by zhengqibonan 8 months ago - 1 comment

#793 - resident size (66266557647) exceeds memory limit

Issue - State: closed - Opened by zhengqibonan 8 months ago

#791 - v2.1.9 does not output `send` correctly when using long-read mode

Issue - State: open - Opened by xinehc 8 months ago - 2 comments

#790 - Formatted NR database

Issue - State: open - Opened by stephen-14 9 months ago - 2 comments

#789 - Inconsistent Percentage of Identity Calculations with 'X' Characters in DIAMOND BLASTP Output

Issue - State: open - Opened by nvucic 9 months ago - 1 comment

#788 - Inconsistent taxonomy assignment results for the same sequences

Issue - State: open - Opened by XHe20 9 months ago - 1 comment

#787 - About the '--masking 0' option

Issue - State: open - Opened by ZhangBioLab 9 months ago - 2 comments

#786 - Segmentation fault at stage of joining output blocks

Issue - State: open - Opened by charlesfoster 9 months ago - 2 comments

#785 - Segmentation fault (core dumped) in V2.1.9

Issue - State: open - Opened by miparrama 10 months ago - 11 comments

#784 - read numbers in diamond input, output and Megan "no hits"

Issue - State: open - Opened by rocherbpb 10 months ago - 1 comment

#783 - The lengths of sseq and qseq in the output results of diamond blastp are inconsistent

Issue - State: closed - Opened by ZhangBioLab 10 months ago - 4 comments

#782 - Question: Force all vs all alignment?

Issue - State: closed - Opened by paoslaos 10 months ago - 2 comments

#781 - Question about min-orf change for blastx in v2.1.0

Issue - State: closed - Opened by Stikus 10 months ago - 4 comments

#780 - ERROR: : double free or corruption (!prev) and free(): corrupted unsorted chunks

Issue - State: open - Opened by hans-vg 10 months ago - 3 comments

#779 - Diamond Windows Installation Question

Issue - State: open - Opened by CW1211 10 months ago - 3 comments

#777 - Command line options

Issue - State: open - Opened by saassli21 10 months ago - 1 comment

#776 - colnames and EC number

Issue - State: open - Opened by SueFletcher 10 months ago - 7 comments

#775 - Diamond Windows Installation

Issue - State: closed - Opened by parsanayyara 11 months ago - 4 comments

#774 - Building reference seed array error

Issue - State: open - Opened by kmanoharan01 11 months ago - 1 comment

#773 - Genetic code start codon variation

Issue - State: open - Opened by cmayer 11 months ago - 1 comment

#772 - Error: Gap penalty settings are not supported for this scoring matrix.

Issue - State: open - Opened by cmayer 11 months ago - 1 comment

#771 - Fix build with clang 17

Pull Request - State: closed - Opened by Jehops 11 months ago

#770 - --cluster-steps parameter set as 'sensitive' in clustering

Issue - State: open - Opened by AMbioinformatics 11 months ago - 4 comments

#769 - Build failure on FreeBSD CURRENT after import of llvm/clang v17

Issue - State: open - Opened by Jehops 11 months ago - 2 comments

#768 - Diamond and frameshifts in longer hits. Different results in Blastx vs Blastp [Bug]

Issue - State: open - Opened by Thernn88 11 months ago - 2 comments

#767 - what parameter i should set to filter out all bacterial blastp results?

Issue - State: open - Opened by terancehhwong 11 months ago - 3 comments

#765 - how to make a diamond-formatted KEGG database with taxonomic information from NCBI and KEGG brite?

Issue - State: closed - Opened by terancehhwong 11 months ago - 1 comment

#763 - Diamond not able to detect repeats?

Issue - State: closed - Opened by gandarath 12 months ago - 7 comments

#762 - About the running times

Issue - State: open - Opened by KJ-Ma 12 months ago - 2 comments

#761 - difference between qcov (ncbi blast) and qcovhsp (diamond blast)

Issue - State: open - Opened by terancehhwong 12 months ago - 9 comments

#760 - output file missing even though diamond works seemingly fine

Issue - State: closed - Opened by terancehhwong 12 months ago

#759 - Error: Database file is not a BLAST database

Issue - State: open - Opened by lida56 12 months ago - 5 comments

#757 - diamond blastx support for IUPAC ambiguity code

Issue - State: open - Opened by wiebepo 12 months ago - 1 comment

#756 - DNA letter check logic

Issue - State: open - Opened by ftegenfe almost 1 year ago - 1 comment

#755 - Error: Input file is not a DAA file

Issue - State: closed - Opened by katievigil about 1 year ago - 9 comments

#754 - Quick question about data availability

Issue - State: closed - Opened by onsi about 1 year ago - 2 comments

#753 - Sequences apparently masked even when masking is disabled.

Issue - State: closed - Opened by ojanson about 1 year ago - 2 comments

#752 - difficult genome with repeated genes fails to self-align

Issue - State: open - Opened by stubrown about 1 year ago - 1 comment

#751 - Inconsistent numbers of hits across split databases

Issue - State: open - Opened by daron-m-standley about 1 year ago - 5 comments

#750 - LCA taxomic classification: minimal example

Issue - State: open - Opened by danpal96 about 1 year ago - 2 comments

#749 - Taxonomic families

Issue - State: closed - Opened by katievigil about 1 year ago - 8 comments

#748 - Diamond returns longer queries than the targets it was mapped against.

Issue - State: open - Opened by Thernn88 about 1 year ago - 1 comment

#747 - Diamond Clustering randomly crashing.

Issue - State: open - Opened by Thernn88 about 1 year ago - 1 comment

#746 - Blast running in a loop for nanopore data

Issue - State: open - Opened by bioinfo23 about 1 year ago - 1 comment

#744 - install diamond

Issue - State: open - Opened by vahidodin about 1 year ago - 3 comments

#739 - Does Diamond support DNA sequence (that cannot be translated into protein) alignment?

Issue - State: open - Opened by simon19891216 about 1 year ago - 3 comments

#735 - Paired end fastq queries exit with "Error: Unequal number of sequences in paired read files."

Issue - State: open - Opened by ryandkuster about 1 year ago - 2 comments

#719 - Issue with loading taxonomy names in Diamond

Issue - State: open - Opened by joseailtoncruz over 1 year ago - 14 comments

#680 - `prepdb` not working in v2.1.4

Issue - State: closed - Opened by xinehc over 1 year ago - 4 comments

#651 - GLIBC not found

Issue - State: closed - Opened by katievigil almost 2 years ago - 6 comments

#643 - Protein alignment an taxonomic binning with DIAMOND v2.0.15 and Megan

Issue - State: open - Opened by alicaheid almost 2 years ago - 3 comments

#629 - How to estimate the memory requirements for Diamond given the database and query protein sizes?

Issue - State: open - Opened by jolespin almost 2 years ago - 4 comments

#615 - Add NEON implementation for `armv7` and `aarch64` platforms

Pull Request - State: closed - Opened by althonos about 2 years ago - 6 comments

#526 - makedb process issue. Error: Inflate error.

Issue - State: open - Opened by Edward-Tristan about 3 years ago - 2 comments

#495 - makedb (Error: Tokenizer Exception)

Issue - State: closed - Opened by kabilov over 3 years ago - 5 comments

#439 - Support for BLAST databases

Issue - State: open - Opened by bbuchfink over 3 years ago - 27 comments
Labels: experimental

#429 - Diamond makedb issue: invalid characters

Issue - State: closed - Opened by pinocytosis0513 almost 4 years ago - 1 comment

#422 - please reconsider default value for "--threads" or at least specify it in the help function

Issue - State: open - Opened by jvollme almost 4 years ago - 5 comments

#356 - Diamond -> MEGAN with long reads

Issue - State: closed - Opened by devindrown over 4 years ago - 14 comments

#352 - Error: Invalid taxonomic rank

Issue - State: closed - Opened by 473021677 over 4 years ago - 6 comments

#301 - Full_sseq returns sequence with N or X

Issue - State: open - Opened by MarHerf about 5 years ago - 6 comments

GitHub / bbuchfink/diamond issues and pull requests