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SPAdes Genome Assembler
Hi all, I'm using paired-end assembly on GAGE-b MiSeq dataset. (--pe-1 r1.fastq --p2-2 r2.fastq) In the log file, I found "**Skipping processing of scaffolds (empty file)**" and the output therefore...
Error 20
Hi, When I run spades for a group of samples I keep on getting the following error mesages ======= SPAdes pipeline started. Log can be found here: /n/scratchlfs/buenrostro_lab/sam_rotation/assemblies/SRR5983368_ms_out/spades.log ===== Read...
I have run MetaSpades with all 99 other samples. With this sample it has finished abnormally with err code: -11. I have already rerun it 3 different times. Please advise,...
I'm running cloudspades with simulated metagenomes (10 reference genomes per metagenome, 1 mil paired-end SLR reads, reads simulated via ART). I'm using the following command: ``` spades.py --meta -k auto...
I'm trying to assemble some publicly available metagenomic data using metaspades. The data is here: https://www.omicsdi.org/dataset/omics_ena_project/PRJNA379494. I'm testing the first set of paired-end reads: SRR5351712_1 and SRR5351712_2. I was able...
Hello, I want to use **metaspades.py** to assemble the **metagenomic datasets**. The metagenomic sequencing was performed using illumina platform (**2×150, insert size is about 380bp**). Adapter sequences were removed from...
Hi! I'm using SPAdes for a while already, and until today it worked perfectly. I use it to assemble genomes of small viruses (less than 5kb) from enriched samples. I...
Hi there, I'm looking for the two datasets named in the title. This link - http://data.cab.spbu.ru/index.php/s/tz7mCqDipgbcsbW - shown in the paper - https://genome.cshlp.org/content/29/6/961.full, results in a file not found error....
Hi developers, I'm assembling an eukaryotic genome with SPAdes 3.13.1 and ran into err code: -11 after K21: ``` 0:43:49.631 26G / 35G INFO K-mer Index Building (kmer_index_builder.hpp : 301)...
Hi, I am trying to assemble the plant mitochondrial genome with Illumina pair-end and nanopore reads. I assembled in two approaches. 1. Assembled all reads by denova assembly. 2. Removed...
