Kraken2 github

Kraken2 github. Nov 23, 2021 · Saved searches Use saved searches to filter your results more quickly You signed in with another tab or window. Designed and maintained by Ben Siranosian in Ami Bhatt's lab at Stanford University. My kraken2-build command has been running for a few days (building a ginormous database), but I noticed that it's been "stuck" here since at least this morning. Building Kraken2 database issue. Feb 18, 2020 · I tried kraken-translate on the kraken2 output and received the following error: kraken-translate: command not found. Creating sequence ID to taxonomy ID map (step 1) Found 185976536/188119403 targets, searched through 731540803 accession IDs, search complete. I run kraken2 with --memory-mapping while put database on disk. nashanghenzan opened this issue on Feb 23, 2023 · 1 comment. com Cc: Maria Sardi Maria_Sardi@cargill. o Jan 3, 2021 · Unfortunatelly, it's a bit too large, I'm trying to run kraken2 on Jetson Xavier NX and Jetson Nano, which have 8 and 4 GBs of memory, respectively. Regardless, below is the command i submitted Sep 12, 2021 · Just provide your fastq files full name and check that there is no typo and that the actual fastq files that you provide in your kraken2 command are accessible (for example : more your_file. Typically, the installation process involves downloading the source code from the Kraken2 GitHub repository and compiling it on the user's system. One-time loading of databases (a slow step compared May 20, 2019 · Sign in to comment. sh zhaohui_kraken2 make: Entering directory /proj/barc/users/z Yvain-Desplat commented Jul 13, 2021. Hi Derrick, I tried classifying my sample reads with kraken database containing only "nt" sequences and found that all my reads were classified at the root. Downloading nucleotide wgs accession to taxon map done. Apr 28, 2023 · Titch123 commented on Apr 28, 2023. Otherwise it will fetch the nucleotide accession2taxid files from Ncbi - leading to the problem of unmapped ids Nov 3, 2020 · I have a problem after using building kraken2 database. The other needs to be the desired level, like G, S, P, G1 etc Output file will be placed into the input directory. Sep 2, 2022 · When I run kraken2-build --standard --db krakendb this occured: Downloading nucleotide gb accession to taxon map done. dmp files (and kraken 1 installed), you can run the following: touch database. com; Author author@noreply. Already have an account? Jan 15, 2019 · Read length. " Has support for this feature be Saved searches Use saved searches to filter your results more quickly Mar 31, 2020 · Many taxa are not represented in the plants genomes database (that I think Kraken2 uses for the 'plants' database build). In order to facilitate efficient and reproducible metagenomic analysis, we introduce Kraken Protocols, an end-to-end pipeline for the classification, quantification, and visualization of metagenomic datasets. /Kraken2_Database/ --threads 40 &>. This command will create one file, containing the OTUs of given level. --threads 100" submitted by bsub. Downloaded acces Simple Kraken2 Nextflow pipeline. Second, I would also use --minimum-hit-groups 3 (or 4) when running kraken2, which minimizes false positives resulting from the minimizer compression we use in the kraken 2 database build. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. Oct 6, 2018 · tseemann commented on Oct 6, 2018. fastq). Already have an account? Jul 11, 2022 · Hi Everyone， Because there are so many unclassified (>80%) reads, so I want to extract the unclassified reads using the code as below, it report error: classify: Paired filename format missing # character, How to slove? Jan 20, 2021 · There used to be some non-deterministic parts to the kraken2 database build but we have fixed that now. 1, 0. Thanks for the steps given for downloading the database. Sep 29, 2022 · Kraken2 is a software that matches each k-mer of a query sequence to the lowest common ancestor of all genomes containing the k-mer and classifies it into a taxonomic tree. Building Kraken2 database issue #303. After sitting for 6 days at the same point (the number of sequences processed Dec 26, 2019 · Yes, Kraken is intended to work with DNA input and so also has to handle the possibility of data from either strand being read there. Did you manage masking the final dabatase? I'm using it with the three steps given (1. download assembly file; 2. In the kraken2 report, I get 9 millions Number of raw reads, while I expect to see twice as there are 2 fastqs of 9 millions reads each. #709. Aug 10, 2021 · jessicarowell commented on Aug 10, 2021. Projects. No k2mask in path. Jan 8, 2020 · We do not have a separate script for kraken2 at the moment but if you do have the taxonomy/ folder with the nodes. Sep 16, 2020 · Running kraken2-build --download-library human fails at it appear to write to assembly_summary. I don't know why it happened, the fallowing is detail. Apr 13, 2020 · Hi there, I am seeing very low mapping rates (~10-15%) for my whole genome sequencing data using Kraken 2. This project builds on the classification functionality to provide a server-client architecture to allow two use cases: Access to the classification algorithms in low-resource settings by sending requests to remote, more powerful servers. The current official version of Kraken 2 is v2. Motivation. Open. g. 7-beta commmand line: nohup kraken2-build --download-library human --db . 8-beta (released April 25th, 2019). MANZHAOHUI commented on Nov 12, 2020. Jul 19, 2023 · Saved searches Use saved searches to filter your results more quickly Jul 24, 2018 · I don't have access to an old implementation of glibc; if the following code is added to the end of kraken2_headers. The nt database is fairly large and building can take awhile especially if done single-threaded. I have since downloaded the ncbi taxonomy and the original fna se Jul 20, 2021 · Hello, I'm working with a metagenome and I'm not sure what is better if using kraken2 with the output from the MEGAHIT (contigs) or using reads (paired). The material I have used Kraken2 to analyze previously came from metagenomic sources and it is clear that we frequently get reads mapping to sister taxa when the Jun 13, 2019 · Assignees. OUTPUT > KRAKEN2. The default is 2, but I've found more success with a Feb 22, 2023 · when I write kraken2-build --build --threads 15 --db . It seems there is something wrong with the recent conda builds of kraken2. The data processed in my work is single-ended sequencing data. Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. I've tried building database with only one library, but it seems like the hash. 645. Source (99 KB): Kraken2's source code and README. ~80% of these were classified as Bacteria (the majority of which were known to be associated with plants, so it made sense), and the other ~20% were generically classified as “cellular organisms”. I'm struggling because the contigs are large (min length is 1000 bp) and I don't kn Dec 9, 2022 · I have placed kraken2, kraken2-build and kraken2-inspect in my PATH. I followed the manual and successfully installed kraken2 and copied the main scripts to my bin (as is shown below) (base) [zhaohui@longleaf-login1 KRAKEN2]$ . downloaded nr DB properly, parsed sequences, masked low diversity all good but when building the database I get the following: kraken2-build --build --db nr-ncbi/ --threads 80 Creating sequence ID to taxonomy ID map (step 1) Jun 24, 2020 · Same question occured to me recently. 5 and 1. This is what I run and what I get (database is specified in an env variable): $ kraken2 --report --output k2-test/kreport. REPORT. txt ├── library. I want to build a kraken database: kraken2-build --standard --threads 24 --db krakendb This line seems to work until this step: Step1/2: performing rsync file transfer of requested files The exit message reads: [Receiver] io timeout afte Jul 13, 2019 · My command is: kraken2-build --download-library bacteria --db krakenDB --threads 20 --use-ftp I go back to the log files and I get this: Step 1/2: Performing ftp file transfer of requested files Dec 27, 2021 · jenniferlu717 added the download issue kraken2-build --download-library issue label Mar 14, 2022 Sign up for free to join this conversation on GitHub . It's important to ensure that all dependencies are met and that the environment is properly configured for Kraken2 to function correctly. I have confirmed that I have the permissions to execute the file. I find simple parsing of kraken2 output report can be a bit annoying. kraken2. Star 645. I would like to add fungal identification to my analysis, so I would like to replace the standard kraken2 database with the PlusPF. parse_kraken2_report. I have reserved 2 nodes with 44 cores each and execute kraken2-build with the command below: kraken2-build --build --db test --thread Jun 3, 2021 · Hi,when I use kraken2 to build nr database, it shows no miastake but seems stopped. Pull requests 16. To associate your repository with the kraken2 topic, visit your repo's landing page and select "manage topics. My fastqs have 9 millions each. Reload to refresh your session. kraken Dec 17, 2021 · Kraken. 2$ kraken2-build --standard --threads 64 --use-ftp --db kraken_db However, the command created a directory "kraken_db" with Oct 20, 2020 · So I first took these potential rRNA reads and used Kraken2 against the full Standard database. Jul 16, 2019 · kraken2-build --download-library fungi --db fungi But when I performed kraken2-build --build --db fungi it appears an error: Can't find taxonomy/ subdirectory in database directory, exiting. 8_beta. pl -names names. I think the critical part is to apply the --protein option already for the --download-taxonomy job. For this, I edited /etc/fstab to allocated 55g of RAM, more than enough to hold the Standard database (tmpfs /dev/shm tmpfs size=55g 0 0) Copy the *. Here you have 0 processed sequences which means in my opinion that kraken2 is not even able to access the sequences in your file. 0. Kraken does NOT differentiate between forward and reverse strand data, however, so you will not be able to get or use any sort of strand-specific information. gz compression is the issue since they're all zipped, and some work while others don't, but I'll try --gzip-compressed and see if that makes the difference! Aug 13, 2020 · Hi is there any solution to this problem, when i run this command line kraken2-build --build --db database it prompts: Creating sequence ID to taxonomy ID map (step 1) No preliminary seqid/taxid mapping files found, aborting. Dec 22, 2019 · I am using the latest version of kraken2 on centos 6. I tried to re-run my pipeline which is using Kraken2 (I ran it as near as last week on the same data and it was working fine), however I got a following error: libexec/classify: invalid option -- 'H' As you can see below, my command does Mar 31, 2023 · No k2mask in path #709. Sign up for free to join this conversation on GitHub . Kraken2 is a taxonomic sequence classification system. Abstract. To evaluate the correlation between the size of input data and time consumed, I splitted the orignal data to 50 parts (total line number of each parts % 4 = 0). If you parse only using the percentage/number of reads assigned, then you end up not only with Salmonella enterica but also everything between Salmonella enterica and root. In other words, provide all options (--use-mpa-style, --report-zero-counts) before you provide the two sample files and then the > original_1. The tree file is the following one: fungi/ └── library └── fungi ├── assembly_summary. I downloaded this database and it only includes the hash. Introduction. Contribute to maxibor/kraken-nf development by creating an account on GitHub. Here is the output from the first few lines of the report file: 100. (note - species = S, subspecies = S1, varietas = S2 in kraken) ] D. Here is the output: Creating sequence ID to taxonomy ID map (step 1) Dec 26, 2019 · to join this conversation on GitHub . aebordoy opened this issue on Mar 31, 2023 · 2 comments. The only thing missing is the final summary. k2d and the taxo. Feb 8, 2022 · I am having the same issue as stated in #534with the NT database build. . 01, 0. Oct 11, 2022 · Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e. · Issue #428 · DerrickWood/kraken2 · GitHub. taurus 5S rRNA gene4W1Z_7 Chain 7, Structure Of The Mammalian 60s Ribosomal Subunit (this Entry Contains The Large Ribosomal Subunit Rna)4W21_7 Chain 7, Structure Of The 80s Mammalian Ribosome Bound To Eef2 (this Entry Contains The Large Ribosomal Subunit Rna)4W24_7 Chain 7, Structure Of The Idle Mammalian Ribosome-sec61 Complex (this Entry Contains The Large Ribosomal Subunit Rna Oct 9, 2021 · I have same issue. run rsync command; 3. The Kraken2 GitHub repository provides the latest updates, news, and downloads for the software. I have had kraken2 standard installed for a couple of years and have used it with no issues. Hi all, I am interested in using KrakenUniq with kraken2, specifically the --report-minimizer-data. 56xlarge, 224 threads, 6144 GB RAM, using CentOS 7). k2d, opts. #303. javad30 opened this issue on Jun 11, 2023 · 3 comments. github. I not Nov 21, 2019 · Oh you should also be using --protein when you run kraken2-build --build: kraken2-build --build --db kraken2/ --threads 30 --protein. kdb touch database. k2d files. Quick Start. It uses minimizers, spaced seeds, and protein or 16S databases to achieve high accuracy and fast classification speeds. Notifications. You signed out in another tab or window. 00% 14552 14 Jun 21, 2021 · Saved searches Use saved searches to filter your results more quickly Sep 15, 2020 · Sign in to comment. " GitHub is where people build software. I have built a database containing archaea, bacteria, human, fungi, viral, nt, env_nt, plant, plasmid. sh at line 125 and 128 as below. Hi developers, I'm am trying to run Bracken using a custom Kraken2 database. Taxonomically informed parsing of kraken2 report output. zip $ kraken2-build --standard --threads 12 --db kraken2db/ Downloading nucleotide gb accession to taxon map done. That database maps k -mers to the lowest common ancestor (LCA) of all genomes known to contain a given k -mer. Jun 8, 2019 · "$ kraken2-build --download-library bacteria --db refseq_bacteria" But when I try to build the database with "$ kraken2-build --build --db . dmp and names. 1 and my command is "kraken2-build --build --db . We hope to have a script for this soon. Even if selecting y to overwrite, the move fails: mv: replace 'assembly_summary. /, finally I just got two files in my directory: seqid2taxid. The task runs very very slow, not finished after two hour. Jul 18, 2022 · I've got the --paired flag, and I don't think the . Run kraken2 with --memory-mapping. k2d is just never populated, it always stays the same (empty), even if sequences are processed (seemingly) correctly. DerrickWood / kraken2 Public. Apr 26, 2021 · DJFast commented on Apr 26, 2021. idb touch database. You switched accounts on another tab or window. dmp -taxa NAME -parent XXX -rank NAME -division X. nashanghenzan closed this as completed on Feb 24, 2023. I could not run any of the available conda builds for version 2. Take note of the ID assigned to each new taxa as it is added. Kraken version 2. k2d files from the database to /dev/shm. The second version of the Kraken taxonomic sequence classification system - Issues · DerrickWood/kraken2 combined. Note: Use of any older kraken2 versions may contain bugs that were Mar 9, 2021 · Kraken2 custom db · Issue #423 · DerrickWood/kraken2 · GitHub. However, when I use the command as described in the manual I get "Unknown option: report-minimizer-data. dmp -nodes nodes. I used a very large AWS ec2 instance to try to build the NT database (u-6tb1. The database location is set for my scratch directory, which i believe has 15TB of space available. The code will run and seems to be able to find the files I need, but says there are 0 sequences. It gets to a point in processing the sequences and then it stalls. mpa: combined kraken2 report in mpa (MetaPhlAn) format; combined_bracken: contains the combined bracken outputs (one file for each taxonomic level, from Domain D to Species S); combine_bracken_reports: same as combined_bracken but in kraken2 report format; A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysis, plots, compositional data and differential abundance calculation. 1 B. I have tried built both standard and custom database with archaea and bacteria library but both process I haven't get any of these three files. Nov 5, 2020 · You signed in with another tab or window. h, would that solve your compilation problems? If so, I think that's a fix I can easily commit. Bracken can estimate abundance of species within a sample). Sample names will be the filenames without extension. Oct 24, 2022 · In the recent Kraken suite paper, the authors outline two workflows: microbiome analysis, and pathogen ID. Dear developers, Kraken1's translate feature produced an incredibly useful summary of the taxonomy of each sequence by providing the full taxonomic lineage (e. report: combined kraken2 report; combined. fna. MY kraken2 version is 2. #81. k2d. The idea is to use the ‘for’ command which would ignore signal 13 instead of the 'xargs' command. kraken file should be at the end of the command line. 7 participants. Hello, I am running kraken2 across illumina paired-end fastqs. I would expect reads to map to other members of the Phylum. Sep 25, 2020 · The sequence files and the pipe to the original_1. masked Nov 26, 2020 · >X57170. Kraken 2 Code Download. /kraken2-build_human. --threads 20" I get following message: "Can't find taxonomy/ subdirectory in database directory, exiting. /install_kraken2. com Subject: Re: [DerrickWood/kraken2] Problems adding genome to database - Prevotella Copri [EXTERNAL] This email came from outside of Cargill Oct 9, 2021 · TonyMane commented on Sep 19, 2021. Fork 259. Issues. Actions. I've run the commands kraken2-build --threads 8 --download-taxonomy --db all_bac kraken2-build --download-lib Jun 3, 2020 · Sign in to comment. Jun 11, 2023 · Kraken Database · Issue #730 · DerrickWood/kraken2 · GitHub. log & Retrun errors: Step 1/2: Performing rsync file transfer of requested files rsync er May 21, 2019 · After that, running kraken2 with --memory-mapping options became very efficient, every task finished within 1 min. KRAKEN2. $ kraken2-build --build --db yyDB --threads 12. Hello, I installed kraken 2 with bioconda and tried to download the standard database like this: (kraken2) bash-4. I recall @jenniferlu717 said there was a minikraken2 database being made available at some point? Any update on this? Would help a lot to get people installing tools dependent on kraken2. fna ├── library. However, additional fixes/changes are in the newest github version. Kraken examines the k -mers within a query sequence and uses the information within those k -mers to query a database. But when I learned that memory-mapping should use mmap function, and the software itself will handle it. txt. Creating sequence ID to taxonomy ID map (step Nov 7, 2019 · So whether by redirect or using the --output (or just letting it scroll) kraken2 does most of the job, looking at a kraken1 run. Jun 9, 2022 · Hi!! @BenLangmead @bgruening @Phhere I am getting this error: kraken2: --paired requires positive and even number filenames when I am providing this command to the system: kraken2 --use-names --db Dec 8, 2019 · Hi Derrick, This issue has been raised previously, but does not appear to have been resolved. Hello I'm trying to create the standard Kraken 2 database, with the following command: kraken2-build --standard --threads 16 --db kraken-Sdb I'm getting this: Step 1/2: Performing rsync file transfer of requested files Rsync file transfe Jul 27, 2018 · ajaybabu27 commented on Jul 27, 2018. #692. Was kraken-translate added into kraken2? The manual says the report flag has replaced the functionality, however, I will have to manually translate the tax ids to lineages in the full output and remove all the other kmer Sep 3, 2020 · I need use kraken2 on PBS task management system. So if the RAM is unstable, I will be in big trouble. scan_fasta script), then I used kraken2-build --build to build the dabase, however, the masking step is also important : Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (column 2 in summary) - npbhavya/Kraken2-output-manipulation Aug 14, 2020 · I am using kraken2 to build a custom database on a Cray XC40/50 high performance computing environment. Run taxdump_edit. For the download of taxonomy i used: kraken2-build --download-taxonomy --db database charlesfoster commented on May 19, 2021. "Your calculated TaxID = 3304349. map and taxo. 1. So if someone could point me to some suggestions I can try Assignees. Development. I downloaded the tar ball from the Index Zone page. Downloaded accession to taxon map(s) Downloading taxo Jul 9, 2020 · You should likely run the kraken2-build --build command again using multiple threads. Feb 27, 2020 · -MIS From: Jen Lu notifications@github. " Any ideas what might by causing this? Thanks in advance, Bart Feb 24, 2023 · Loading database informationKilled #692. Make sure /dev/shm has enough space allocated. Just wanted to share in case anyone else encounters the same issue. txt multiple times. If you Nov 29, 2020 · You signed in with another tab or window. Greetings, trying to build default genomic data-bases used to run kraken2 on an HPC cluster. Here are the steps that produced the error: Masking low-complexity regions of new fileError: (CObjReaderParseException::eNoResi Apr 20, 2021 · A space will not work) C. This status continued more than three days. cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria). Apr 28, 2021 · Dear @ther4pture,. srisvs33 opened this issue on Aug 29, 2020 · 2 comments. Jan 19, 2021 · Perhaps what I am about to describe goes against the accepted method for adding to a new kraken2 database. Samples are gut microbiome samples from patients with heart disease, sequenced on Illumina HiSeq X, paired end 150bp, 350 bp inser Oct 22, 2018 · I probably solved it by editing build_kraken2_db. Mar 27, 2021 · Kraken2 database building stalls at some point. For the microbiome workflow, it is not tagged as optional, but the language still makes it sound optional ("Depending on the source of the metagenomic sample Jan 23, 2022 · You signed in with another tab or window. the kraken2 version. For github issues, it may also be helpful to provide the output of kraken2-inspect : kraken2-inspect --db MYDB > k2inspect_output. 7_beta and 2. sankadinesh opened this issue on Jan 15, 2019 · 7 comments. The "Host Removal" step is said to be optional for the pathogen ID workflow. the command line used ( kraken2-build or kraken2) the database being used. jdb kraken-report --db . Mar 1, 2020 · No milestone. Loading database informationKilled. tmp. The source code for the current release and the newest version are both available at the Kraken 2 GitHub repository. I built a custom database which appears to have built as expected: Creating sequence ID to taxonomy ID Feb 9, 2021 · Nathalia-Cavichiolli commented on Feb 9, 2021. txt', overriding mode 0555 (r-xr-xr-x)? y mv: cannot move 'x' to 'assembly_summary. No branches or pull requests. kraken2-build --build --db nt --threads 16 'Estimated hash table requirement: 345259953004 bytes' Taxonomy parsed and converted. Sep 12, 2019 · jhcaddisfly on Sep 12, 2019. However, this blocks the --report switch, and I still haven't figured out how to reproduce that functionality. I tried to build using sudo permissions, but no luck again. I also tried to set the --threads 1, but it didn't work. Our protocol describes the execution of the Kraken programs, via a sequence of easy to use scripts, in two scenarios: (1 Jan 24, 2019 · Hello, I have been trying to follow the steps to generate a kraken2 db of all bacteria. txt': Permission denied "kraken2-build --download-library human --db Jul 31, 2019 · Try using Kraken2 with the --confidence parameter and using the Bracken algorithm also Hi @pedrocr83 ive tried with the --confidence parameter with 0. When submitting a github issue, specify. com Sent: Thursday, April 9, 2020 10:08 PM To: DerrickWood/kraken2 kraken2@noreply. Hello, I am having trouble getting Kraken2 to accept my input files (gzipped paired end fastq in separate files). I expect it to count up the number of processed sequences One argument is the directory, where kraken2 reports can be found. Closed. However, I have used these files on SqueezeMeta without a problem. Already have an account? Kraken version 2. ea wn ks ma jr bc vb yb pe wi