spades

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no contig files on metaspades run, but no error in log file

4

### Description of bug When I run `metaspades.py` via a conda environment, the process will run but no contig files are created. I seem to get all the intermediate files....

ewissel

metaviral fails without error notification

11

I'm running metaviral SPAdes with low-complexity (2-5 viruses) samples, and while it successfully works with most of them, three of them are consistently failing without warnings. The logfile reports no...

geboro

metaSPADES out of memory errors on medium size dataset

13

### Description of bug I am running metaSPADES on a co-assembly of 6 samples totalling 19gb raw reads given to metaSPADES. Despite this being a somewhat typical size of metagenomic...

Rob-murphys

metaSPAdes stuck on read error correction

26

I've been running metaSPAdes on my dataset for about one week but it looks to be stuck on the error correction step of the pipeline and hasn't progressed since. I...

kevinxchan

[build error report] lto

3

### Description of bug See here: https://build.bioarchlinux.org/api/pkg/spades/log/1658750629 ``` [ 92%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta [ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o [ 92%] Linking CXX executable ../../bin/spades-truseq-scfcorrection [ 92%] Linking CXX...

alienzj

Failed to determine read length for library #0 for IonTorrent data

6

### Description of bug Hi! I'm a smidge baffled and can't find a solution online. I'm trying to assemble five IonTorrent single read datasets. The read correction worked just fine...

samche42

Spades-hammer stuck on reverse reads

5

When running metaspades on a paired-end FastQ files with error correction enabled, `spades-hammer` process through counting the k-mers on the forward reads, but gets stuck on doing the same on...

alexhbnr

finished abnormally, err code: -9

3

### Description of bug == Error == system call for: "['/soft/SPAdes-3.13.0-Linux/bin/spades-hammer', '/scr/manuel/Marina_scr/seq_TS/otros/SPADES_TS_oct/corrected/configs/config.info']" finished abnormally, err code: -9 ### spades.log [spades.log](https://github.com/ablab/spades/files/8831812/spades.log) ### params.txt [params.txt](https://github.com/ablab/spades/files/8831814/params.txt) ### SPAdes version SPAdes v 3.13.0 ###...

marina-vn

spades-hammer finished abnormally, OS return value: -7

7

### Description of bug Dear Spades Team, I'm getting this spades-hammer error after 38 hours of metaspades assembly process. ####### == Error == system call for: "['/nobackup/fbsev/bioinformatics-tools/SPAdes-3.15.4-Linux/bin/spades-hammer', '/nobackup/fbsev/LeedsOmics/DougStewart-Jan22/metaWRAP-run/ASSEMBLY_A/metaspades/corrected/configs/config.info']" finished abnormally,...

eltonjrv

== Error == system call for: "['/srv/conda/envs/de_novo_example/share/spades-3.11.1-4/bin/spades', '/home/jovyan/genomics_de_novo_temp/working_dir/spades_default_assembly/K21/configs/config.info']" finished abnormally, err code: -9

9

### Description of bug Hello Good day. I am Paula Maza and currently working on a microbial metagenomics dataset. I am new to shotgun metagenomics and hoping to learn along...

paulamaza