Increase memory limit in SPAdes-3.6.1

Question

[ashaneev07]

Hiii... i'm getting the following error while running SPAdes-3.6.1-linux.

vailable memory limit. Increase memory limit and restart

    == Error ==  system call for: "['/home/Documents/TZ/SPAdes-3.6.1-Linux/bin/hammer', '/home/Documents/TZ/SPAdes-3.6.1-Linux/bin/trichochloroassembly1111/corrected/configs/config.info']" finished abnormally, err code: 255

What does it mean???

[shenwei356]

$ spades.py --help
SPAdes genome assembler v3.13.0

...

Advanced options:
--dataset       <filename>      file with dataset description in YAML format
-t/--threads    <int>           number of threads
                                [default: 16]
-m/--memory     <int>           RAM limit for SPAdes in Gb (terminates if exceeded)
                                [default: 250]

[ahaswer]

Can you provide command that you use to run SPAdes? Also keep in mind that the newest version of SPAdes is 3.13.0 and there were some improvements in RAM consumption since 3.6.1 version.

[ashaneev07]

./spades.py --pe1-1 /media/chloroplast_reads/300BP_R1.fastq --pe1-2  /media/chloroplast_reads/300BP_R2.fastq --pe2-1 /media/chloroplast_reads/500BP_R1.fastq --pe2-2  /media/chloroplast_reads/500BP_R2.fastq --pe3-1 /media/chloroplast_reads/800BP_R1.fastq --pe3-2  /media/chloroplast_reads/800BP_R2.fastq --pacbio /media/chloroplast_reads/pacbio.fa  --threads 15 -o assembly1111

The above command was used.Thank you

[ahaswer]

If your machine has more than 250 Gb of RAM then use -m flag with increased RAM limit, as shenwei356 suggested. If you don't have access to more RAM try to run some test runs with modified -k parameter (follow SPAdes manual). Consider running test assembly without PacBio reads. Also you can try to assembly Illumina reads with NOVOPlasty which is designed for mitochondrial and chloroplast genomes assembly (I assume you are interested in plastid assembly).

[ashaneev07]

Thanks for your replay. I limited my inputs and once again ran the program. Now, its finished the pipeline but shows warning messages. I've pasted the command and the warning messeges that i've got.

./spades.py --pe1-1 /media/chloroplast_reads/300BP_R1.fastq --pe1-2  /media/chloroplast_reads/300BP_R2.fastq  --pacbio /media/chloroplast_reads/pacbio.fa  --threads 15 -o assembly112


== Error ==  system call for: "['/home/Documents/Chloroplast_Blast/SPAdes-3.6.1-Linux/bin/spades', '/home/Documents/Chloroplast_Blast/SPAdes-3.6.1-Linux/bin/trichochloroassembly300/K77/configs/config.info']" finished abnormally, err code: -6

======= SPAdes pipeline finished WITH WARNINGS!

=== Pipeline warnings:
 * Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (150) is equal to or greater than 150
=== Error correction and assembling warnings:
 * 0:11:49.354     2G / 3G    WARN    General                 (kmer_coverage_model.cpp   : 328)   Valley value was estimated improperly, reset to 6
 * 0:11:49.358     2G / 3G    WARN    General                 (kmer_coverage_model.cpp   : 367)   Failed to determine erroneous kmer threshold. Threshold set to: 6
 * 0:11:49.363     1G / 3G    WARN    General                 (graph_simplification.hpp  : 670)   Mean coverage wasn't reliably estimated
 * 0:13:48.975     3G / 3G    WARN    General                 (kmer_coverage_model.cpp   : 328)   Valley value was estimated improperly, reset to 4
 * 0:13:48.979     3G / 3G    WARN    General                 (kmer_coverage_model.cpp   : 367)   Failed to determine erroneous kmer threshold. Threshold set to: 4
 * 0:13:23.185     5G / 5G    WARN    General                 (kmer_coverage_model.cpp   : 216)   Too much erroneous kmers, the estimates might be unreliable
 * 0:13:51.504     5G / 5G    WARN    General                 (kmer_coverage_model.cpp   : 328)   Valley value was estimated improperly, reset to 3
 * 0:13:51.507     5G / 5G    WARN    General                 (kmer_coverage_model.cpp   : 367)   Failed to determine erroneous kmer threshold. Threshold set to: 3
======= Warnings saved to /home/Documents/Chloroplast_Blast/SPAdes-3.6.1-Linux/bin/assembly112/warnings.log

[ahaswer]

Check obtained contigs. The warning doesn't necessary mean that your assembly gone wrong.

[ashaneev07]

hi... I'm sorry to inform u that, it didn't generate the output files like contigs.fa, scaffolds.fa,etc. It only created the files from the run with different Kmer values and warning logs.

Answer 1

[Buffo]

It means that spades needs more memory (RAM) than the available, if possible in your computer, increase the memory limit (250 Gb by default).