spades

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Metaviral spades and Iontorrent?

10

### Description of bug When trying to assemble DNA viral samples using the flags `--metaviral` and `--iontorrent`, spades won't generate any contigs, even when running with positive controls which should...

CEJ-R

err code -9

1

### Description of bug Dear developer and community, I am reporting an error -9 that I get when I try to assemble shotgun sequences for Myxomycetes. I have no problems...

cpouchon

Issue assembling contigs; spades-hammer error

11

### Description of bug HI, I am trying to assemble genome skim data, on spades (have tried both installing through conda and through downloading source code and compiling) and every...

Deco313

### Description of bug Trying to assemble IonTorrent data. I launched SPAdes like this: `spades.py -s /mnt/z/WGS_diphtheria/test/k7rj4.fastq -o /mnt/e/L_drive/projects/ecdc_cdiphtheriae/k7rj4 --iontorrent` I get the following error: ``` [...] 0:02:29.794 1491M /...

ejfresch

k-mer counting take too long

1

### Description of bug Hi, I am assembling my sequencing data on a cluster but this step takes me more than 12 hours. Is there any problem with it? ###...

muzi9841

system call for: "['./spades-hammer'] error

1

### Description of bug Hi, I'm getting this error (SPAdes genome assembler v3.15.5)  ### spades.log [spades.log](https://github.com/ablab/spades/files/10942579/spades.log) ### params.txt [params.txt](https://github.com/ablab/spades/files/10942591/params.txt) ### SPAdes version SPAdes genome assembler v3.15.5 ### Operating System...

MaxBai0123

Contigs contain non-ascii characters

4

### Description of bug After de novo assembly of paired end Illumina reads, Spades output contigs/scaffolds that contain non-ascii characters (). The input fast files do not contain these characters....

christianbrinch

finished abnormally, OS return value: -6

2

### Description of bug Hello, after I ran `spades.py --careful -1 fastq/SRR21726401_1.fastq -2 fastq/SRR21726401_2.fastq -o out/3/` It occurred: spades-hammer: /spades/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:297: size_t kmers::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = Seq; traits...

Riverfishstar

finished abnormally, OS return value: -11

7

### Description of bug Hey I have been trying to run spades This is the command i used spades.py --only-assembler -o SPADES_OUT -1 S17_Trimmed_R1.fq.gz -1 S46_Trimmed_R1.fq.gz -1 S62_Trimmed_R1.fq.gz -1 S72_Trimmed_R1.fq.gz...

Soumyadutta-basak

Spades stucks at (chromosome_removal.cpp : 157) 76824 vertices left

4

### Description of bug Spades get stucks at (chromosome_removal). Usually it take 5-10 minutes. However, it is stuck for more than 15 hours. 0:00:25.771 512M / 9G WARN General (chromosome_removal.cpp...

Ahmer1122