spades

spades copied to clipboard

Determining optimal -m Memory and -t Threads setting

7

While trying to run a mammalian (chromosome-specific) assembly with ~20 million reads, stages with k=21 and k=33 complete successfully. Subsequently, the k=55 step fails with `: Error in malloc(): out...

md5sam

spades finished abnormally, err code -6

7

The assembly finished but I got this message: == ERRORs: * system call for: "['/Volumes/ExternalHD500/SPAdes-3.13.0-Darwin/bin/spades-core', '/Volumes/ExternalHD500/spades_K21_25_33_55_C1/K55/configs/config.info']" finished abnormally, err code: -6 Why did this happen? can I change the parameters...

asavelar

Suggestion: Option to mask with N (or case sensitive) regions with low coverage

2

Hi, when using --trusted-contigs it woud be useful to know regions that had closed gaps without coverage in the result or (similar) regions that had less then "threshold coverage" to...

brdido

Advice on Using Moleculo Reads for Scaffolding with Spades

2

Hi Spades makers and users, I'm seeking some advice regarding whether or not to use Moleculo reads with Miseq and Hiseq short reads (both from Illumina) to improve my assembly....

tarunaaggarwal

== Error == system call for: "[~~~]" finished abnormally, OS return value: -7

2

hey, I'm trying to RNAspades on paired Illumina reads which didn't align to my reference. and I'm getting the following error: == Error == system call for: "['/apps/RH7U2/gnu/SPAdes/3.14.0/bin/spades-core', '~/spadesOutput3/K73/configs/config.info', '~/spadesOutput3/K73/configs/mda_mode.info',...

maorkn

spades correction results in ill-formatted reads

5

Hello, I'm trying to assemble some metagenomes downloaded from EBI, and running into issues with SPAdes outputting fastq reads where the quality line is not the same length as the...

rec3141

Spades finished abnormally, err code: -7

4

Hi guys. I am using spades. 3.13.0. When i assembly my test datasets (huge one), I am getting this error Spades finished abnormally, err code: -7 Could some one help...

srisvs33

Error during metaspades error correction only step-Finished abnormally, err code: 1

4

Hi, I am currently using metaSPades v3.12 on our linux server and was running it only for error correction for 2 metagenomes. One of the genomes successfully got error corrected...

cssulliv

metaspades getting stuck at K55 edge information collection step

1

Hi I am trying to run metaspades on some metagenomic samples. SPAdes always gets stuck at a particular step. K55 collecting edge information. It remains stuck here for hours. Can...

arghya1611

err code: -7

14

Hi, I was trying to run spades in linux, but got following error: == Error == system call for: "['/gpfs/home/user/.conda/envs/tormes-environment/share/spades-3.13.0-0/bin/spades-hammer', '/gpfs/data/projects/Denovo_result/corrected/configs/config.info']" finished abnormally, err code: -7 Could you please guide...

lz870718