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3.6 years 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!
Can you take a look at
spades.logand see if you can find something useful there?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!
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.
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.
Depending on the size of your dataset you may not have enough RAM to run this on your laptop.
Hi, I'm running metaspades for metatranscriptome assembly of 3 soil samples with 3 replicates each in server. A Total 9 paired end reads with total approx. size of 122 GB data. This is the error that I'm getting. Can anyone help me with this problem? here's what my spades.log showing error.
== Error == system call for: "['/cabinfs/opt/applications/SPAdes-3.15.3-Linux/bin/spades-core', '/home/ankita/parse_degs/Whole_assembly_metaspades/whole_assembly_metaspades_soil_Sample.out/K21/configs/config.info', '/home/ankita/parse_degs/Whole_assembly_metaspades/whole_assembly_metaspades_soil_Sample.out/K21/configs/mda_mode.info', '/home/ankita/parse_degs/Whole_assembly_metaspades/whole_assembly_metaspades_soil_Sample.out/K21/configs/meta_mode.info']" finished abnormally, OS return value: 2 None
Thank you!
Are you using a job scheduler? How much memory is being assigned to your job?
out of topic but if you have metatranscriptomic reads you should use rnaSPAdes or Trinity. metaSPAdes is not designed for his kind of data