Tag: metawrap

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…

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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…

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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…

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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…

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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,…

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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…

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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…

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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 >…

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