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SPAdes 3.15.5 ERROR in MacOS Monterey: == Error == exception caught: <class 'FileNotFoundError'>

2

### Description of bug This is an issue that only occurs in SPAdes 3.15.5, if I use SPAdes 3.15.4, this problem goes away. It is just a very common assembly...

YuLanSky

Error == system call for: "['/usr/libexec/spades/spades-core', '/home/yushi/project/sample_519/output_dir/spades_assembly/K27/configs/config.info', '/home/yushi/project/sample_519/output_dir/spades_assembly/K27/configs/isolate_mode.info']" finished abnormally, OS return value: -9 None

1

### Description of bug I tried using unicycler's hybrid assembly command to assemble a genome using two short reads (read 1 and read 2) and a long read. After running,...

Phoebeisphoebe

[cloudspades-3.12.0-0]spades-core with K77 finished abnormally, err code: -8

1

### Description of bug I run the cloudspades with 10X genomics linked-reads for several samples. For some samples, the spade-core crashed with error code -8. I rerun the same sample...

ddzhang3

How do I assemble a merged paired-data using spades?

6

### Description of bug I have paired end file from Illumina, eg. AT11B_trimmed1.fastq and AT11B_trimmed2.fastq. I have used BBMerge to merge the two files to get AT11B_merged.fastq and AT11B_unmerged.fastq. How...

roseedwin

Error: [] finished abnormally, OS return value: -9

1

### Description of bug Job is dropping, but I think I should have enough memory. Not sure what else could cause this? == Error == system call for: "['/opt/software/SPAdes/3.15.2-GCC-10.2.0/bin/spades-hammer', '/mnt/ufs18/rs-008/Hausbeck_group/Lukasko/BotrytisDNASeq/CCR7/SPAdes_assemblies/BM16_assembly/corrected/configs/config.info']"...

lukaskon

binspreader issue - error when specifying --path scaffolds.paths

1

### Description of bug Hi, I am trying to run binspreader with a set of binned scaffolds (binned using metawrap). The program works fine using the default settings, however, when...

ebi-jlu8

metaspades warning

1

### Description of bug Error correction and assembling warnings: * 0:00:00.002 1M / 12M WARN StageManager (stage.cpp : 158) No saved checkpoint ### spades.log [spades.log](https://github.com/ablab/spades/files/11486197/spades.log) ### params.txt [params.txt](https://github.com/ablab/spades/files/11486209/params.txt) ### SPAdes...

Lijiake007

Ubuntu 22.04.2 LTS finished abnormally, OS return value: -11

2

### Description of bug There is an Error in the spades log, however I can only click that there is not one. Spades is calling something incorrectly causing the system...

skbrimer

Having too many short contigs

1

### Description of bug I launched a job two weeks ago and it finally completed today. It is a soil metagenome sample which have been preprossed by fastp/bfc (I used...

chtsai0105

Store intermediate de Bruijn data in tmp folder rather than in RAM

1

### Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above. SPAdes (especially metaSPAdes) requests too much memory. Exploring...

yqy6611