== Error == system call OS return value: -9

[andrewisaiah]

Hi,

The spades run has return an Error return value -9. Everything seemed to be working fine prior to the error message. Below is the spades log file.

13:17:05.452 185G / 185G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /export2/home/andrew/Incubation/Peat/metagenome/concatanated/0_rawreads/Anoxic_R1_merged.fastq.gz
13:18:59.599 185G / 201G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 11212655 reads
13:20:56.632 185G / 201G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22947503 reads
13:22:52.818 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 34742220 reads
13:24:56.206 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 46402407 reads
13:27:02.094 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 57801051 reads
13:29:16.681 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 69865822 reads
13:31:31.729 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 81554074 reads
13:33:55.101 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 93013501 reads
13:36:14.755 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 104831003 reads
13:38:33.095 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 116712418 reads
13:40:49.269 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 128377006 reads
13:42:53.722 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 139929359 reads
13:44:52.721 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 151610404 reads
14:08:31.960 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 274620377 reads
14:16:15.919 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /export2/home/andrew/Incubation/Peat/metagenome/concatanated/0_rawreads/Anoxic_R2_merged.fastq.gz
15:00:03.677 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 540243071 reads
15:17:48.539 185G / 202G INFO K-mer Splitting (kmer_data.cpp : 112) Total 627395088 reads processed
15:17:48.566 163G / 202G INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting.
17:56:14.794 163G / 445G INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 17103975968 kmers in total.
17:56:37.214 133M / 445G INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices
18:19:11.108 12G / 445G INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 17103975968 kmers, 12353602312 bytes occupied (5.77812 bits per kmer).
18:19:11.109 12G / 445G INFO K-mer Counting (kmer_data.cpp : 354) Arranging kmers in hash map order
18:28:12.228 267G / 445G INFO General (main.cpp : 148) Clustering Hamming graph.
20:04:02.484 267G / 445G INFO General (main.cpp : 155) Extracting clusters:
20:04:02.484 267G / 445G INFO General (concurrent_dsu.cpp : 18) Connecting to root
20:04:23.370 267G / 445G INFO General (concurrent_dsu.cpp : 34) Calculating counts

== Error == system call for: "['/export2/home/andrew/miniconda3/bin/spades-hammer', '/export2/home/andrew/Incubation/Peat/metagenome/concatanated/6_metaspades_assembly/Anoxic/corrected/configs/config.info']" finished abnormally, OS return value: -9
None

Param and Log file here:
params.txt
spades.log

Any recommendations would be highly appreciative

[asl]

Hello

Your SPAdes job was killed. Likely more information could be found in the system log.

[andrewisaiah]

Thanks I lot. I tried with a smaller file for assembly and it worked. The server I am using cannot handle large co-assemblies as there is not enough RAM space.

[asl]

Great you figured it out!