metaSPAdes de novo assembly error
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4 months ago
Cedrick • 0

Hello. I am running metaSPAdes in Ubuntu terminal for de novo assembly. However, this error is what I always get:

== Error == system call for: "['/opt/spades/SPAdes-3.14.1-Linux/bin/spades-core', '/opt/data/assembly/K21/configs/config.info', '/opt/data/assembly/K21/configs/mda_mode.info', '/opt/data/assembly/K21/configs/meta_mode.info']" finished abnormally, OS return value: -11

Does anyone here know how to fix this issue?

Thank you!

metaspades assembly genome ubuntu • 426 views
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Can you take a look at spades.log and see if you can find something useful there?

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Hi, here's what my spades.log contains:

Command line: /opt/spades/SPAdes-3.14.1-Linux/bin/metaspades.py -t 2 --only-assembler -m 10 -1 /opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_1.fastq -2 /opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_2.fastq -o /opt/data/assembly

System information: SPAdes version: 3.14.1 Python version: 2.7.17 OS: Linux-5.4.72-microsoft-standard-WSL2-x86_64-with-Ubuntu-18.04-bionic

Output dir: /opt/data/assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF

Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_1.fastq'] right reads: ['/opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: [21, 33, 55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /opt/data/assembly/tmp Threads: 2 Memory limit (in Gb): 10

======= SPAdes pipeline started. Log can be found here: /opt/data/assembly/spades.log

/opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_2.fastq: max reads length: 150 /opt/data/clean/oral_human_example_1_splitaa_kneaddata_paired_1.fastq: max reads length: 150

Reads length: 150

===== Before start started.

===== Assembling started.

===== K21 started.

== Running: /opt/spades/SPAdes-3.14.1-Linux/bin/spades-core /opt/data/assembly/K21/configs/config.info /opt/data/assembly/K21/configs/mda_mode.info /opt/data/assembly/K21/configs/meta_mode.info

== Error == system call for: "['/opt/spades/SPAdes-3.14.1-Linux/bin/spades-core', '/opt/data/assembly/K21/configs/config.info', '/opt/data/assembly/K21/configs/mda_mode.info', '/opt/data/assembly/K21/configs/meta_mode.info']" finished abnormally, OS return value: -11

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: /opt/data/assembly/spades.log

Thank you for using SPAdes!

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Looks like you are running this on Windows/WSL. How much memory do you have on your machine? If I was to hazard a guess I would say you are likely running out of memory since only 10G appears to be assignable.

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Hi. My laptop has a RAM of 8GB. If I am running this on Windows/WSL, how should I disable it or run it in Linux? Sorry, I really have no idea since this is my first time using this platform.

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Depending on the size of your dataset you may not have enough RAM to run this on your laptop.

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