Tag: metawrap
I made an error when using metawrap to binning
I made an error when using metawrap to binning 1 my code metawrap binning -o bin_out -t 24 -m 200 -a all_contig/all_merge.fasta –metabat2 –maxbin2 –concoct all_fastq/*fastq Error reported as follows sorting the SRR10492802 alignment file [bam_sort_core] merging from 24 files and 24 in-memory blocks… [E::sam_hdr_sanitise] Malformed SAM header at line…
A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…
A comprehensive genomic catalog from global cold seeps
Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Pl. Sci. 48, 205–231 (2020). Article ADS CAS Google Scholar Al-Shayeb, B. et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature 610, 731–736 (2022). Article ADS CAS PubMed PubMed Central Google Scholar …
Gut Microbiome of Children with Airway Allergic Disease
Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…
Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species
Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, et al. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun. 2023;14:1127. Article CAS PubMed PubMed Central Google Scholar Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, et…
SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline
doi: 10.12688/f1000research.108835.2. eCollection 2022. Affiliations Expand Affiliation 1 Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA. Free PMC article Item in Clipboard John Krapohl et al. F1000Res. 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.12688/f1000research.108835.2. eCollection 2022. Affiliation 1 Department…
Characterization of metagenome-assembled genomes from the International Space Station | Microbiome
Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…
Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands
Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev. 2015;39:203–21. Article CAS PubMed Google Scholar Pointing SB, Belnap J. Microbial colonization and controls in dryland systems. Nat Rev Microbiol. 2012;10:551–62. Article CAS PubMed Google Scholar Ji M,…
KILLER IMAGES WINS TRIP TO FESPA
By Wayne Robinson | 26 April 2023 NSW print and wrap specialist Killer Image has taken out the Ball & Dogget MetaWrap – Are You Australia’s Greatest Wrapper competition, for its Coopers Camo Truck job. Winner: Killer Images’ truck job After receiving an overwhelming number of submissions from across the…
NSW’s Killer Image wins Ball & Doggett Australia’s Greatest Wrapper
After an ‘overwhelming’ number of entries, the winner of Ball & Doggett’s MetaWrap – Are YOU Australia’s Greatest Wrapper? competition is Coopers Camo Truck by Killer Image from Glendenning in Sydney, NSW. “After receiving an overwhelming number of submissions from across the country, judges – Matt Horne (Wrap Studio),…
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article CAS PubMed Google Scholar Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…
FREE TRIP TO FESPA COMP CLOSES MONDAY
By Wayne Robinson | 31 March 2023 Wide format printers eyeing the Ball & Doggett Metamark MetaWrap Competition – seeking Australia’s greatest wrapper for 2023 – with its eye-watering prize of a free trip for two to Fespa in Munich this May, have until this Monday, 3 April, to get their entries…
Australia’s Greatest Wrapper: three judges announced
Ball & Doggett named three expert judges for its Who is Australia’s Greatest Wrapper? competition to find the best wrap design and installation from around the country. The Metamark MetaWrap Competition is accepting entries until 3rd April, 2023. First prize is a trip to FESPA Munich in May 2023. “The…
METAWRAP WINNER TO FLY TO FESPA
By Wayne Robinson | 22 February 2023 Ball & Doggett is launching the Metamark MetaWrap Competition, seeking Australia’s greatest wrapper for 2023, with an eye-watering prize of a free trip for two to Fespa in Munich this May. Metamark Wrap Competition: Free trip to Fespa for the lucky winner This…
Win a trip for two to FESPA, Munich with Metamark and Ball&Doggett!
Calling all wrap artists…Metamark with Ball & Doggett invite you to enter your finest wrap work – any kind of wrap not just cars – and be acclaimed Australia’s best wrapper. The winner and a partner will travel to FESPA in may as a guest of Metamark, stay 4 nights…
MetaWRAP databases on external HDD
MetaWRAP databases on external HDD 0 Hi, dear community, I am trying to perform a metagenomic analysis using metaWRAP on my own PC. I’ve encountered a problem where I need to download the databases for metaWRAP. Still, they are space-consuming and atm I have a small SSD with Ubuntu on…
metaWRAP Alternatives and Reviews (Sep 2022)
Stats Basic metaWRAP repo stats Last Commit about 1 month ago bxlab/metaWRAP is an open source project licensed under MIT License which is an OSI approved license. Truly a developer’s best friend Scout APM is great for developers who want to find and fix performance issues in their applications. With…
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome
Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed PubMed Central Google Scholar Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…
METASnake: a Snakemake workflow to facilitate…
Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…
ERROR [mem_sam_pe] paired reads have different names — during binning in metaWRAP pipeline
ERROR [mem_sam_pe] paired reads have different names — during binning in metaWRAP pipeline 1 I performed the following steps with my data. Performed digital normalization on the individual 205 samples — success removed the host (e.g. human) and adapter sequences from the individual samples — success concatenated the samples into…
failed to run on BwForCluster
I am trying to run metaWRAP on BwForCluster BinAC. I started with Step 1: Run metaWRAP-Read_qc to trim the reads and remove host contamination. I used the following script: #1 :ppn=24 #4:30:00 #9000mb #6 source $HOME/miniconda3/etc/profile.d/conda.sh conda activate metawrap-env cd /beegfs/work/fr_mh1379/metaWRAP mkdir READ_QC for F in Raw_reads/1.fastq; do R=${F%}_2.fastq BASE=${F##1…
Metagenome-assembled genomes: concepts, analogies, and challenges
Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD (2021) A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat Biotechnol 39(1):105–114. doi.org/10.1038/s41587-020-0603-3 CAS Article PubMed Google Scholar Bowers RM,…
Truncated/duplicated genes in Metagenome Assembled Genomes (MAGs) from ONT+Illumina hybrid assembly
Truncated/duplicated genes in Metagenome Assembled Genomes (MAGs) from ONT+Illumina hybrid assembly 0 Hello there, I have performed a metagenome assembly on a single sample using both Illlumina and ONT reads (average q-score 10) with opera-ms. Then contigs were binned using maxbin2, metabat2 and concoct, and metaWRAP was used for bin…
miRDeep2.pl error in make_html2.pl
miRDeep2.pl error in make_html2.pl 0 I have installed cpan install PDF::API2 And still got error Can’t locate PDF/API2.pm in @INC (@INC contains: /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/lib/perl5 /home/nbri/vaishali/TOMATO_SRNA/new_analysis/mirdeep2-master/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64 /perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25. BEGIN failed–compilation aborted at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25 locate PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-0/blib/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-0/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-1/blib/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-1/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-2/blib/lib/PDF/API2.pm…
Metawrap pipeline doesn’t detect samples
Metawrap pipeline doesn’t detect samples 0 Hi, I am running the metawrap pipeline. I have 206 samples that I first concatenated them in 10 groups (A_case, A_control, B_case, B_control, C_case, C_control, D_case, D_control, E_case and E_control), and later into one big paired fastq file as shown below: cat A_case*1.fastq >…
