Tag: metawrap

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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