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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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I have a problem with spades.py #57

Closed lil-bei-bei closed 1 year ago

lil-bei-bei commented 1 year ago

== Running: /Users/yewensheng/opt/anaconda3/envs/Unicycler/bin/spades-hammer /Users/yewensheng/Desktop/015_bar03/assembly_mix/spades_assembly/read_correction/corrected/configs/config.info

0:00:00.000 1M / 7M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/master, git revision 54bed604152fd271b68bdf7b78bfd0788ea9e431 0:00:00.000 1M / 7M INFO General (main.cpp : 76) Loading config from /Users/yewensheng/Desktop/015_bar03/assembly_mix/spades_assembly/read_correction/corrected/configs/config.info 0:00:00.011 1M / 7M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 8 0:00:00.039 1M / 7M ERROR General (memory_limit.cpp : 47) setrlimit(2) call failed, errno = 22

== Error == system call for: "['/Users/yewensheng/opt/anaconda3/envs/Unicycler/bin/spades-hammer', '/Users/yewensheng/Desktop/015_bar03/assembly_mix/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, OS return value: 22

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.

SPAdes log can be found here: /Users/yewensheng/Desktop/015_bar03/assembly_mix/spades_assembly/read_correction/spades.log

Thank you for using SPAdes!

rrwick commented 1 year ago

An issue with SPAdes is outside the scope of this repository, so I'm going to close this one. However, based on the error message, it looks like it might be an issue with memory. Does your computer have enough memory to run this? I'd also recommend you try running SPAdes on its own (i.e. not in Unicycler) to see if it gives you the same error.