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Error during Spades Meta-assembly: err code: -9

Hello there,

I was trying to run a meta-assembly on my Hi-Seq samples and I came across this error:

Command line: /scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades.py  -o  /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades --meta  -t  16  -k  21,33,55,77 --pe1-1 /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq --pe1-2 /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq 

System information:
  SPAdes version: 3.13.0
  Python version: 3.6.3
  OS: Linux-2.6.32-696.6.3.el6.x86_64-x86_64-with-centos-6.9-Final

Output dir: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq']
      right reads: ['/gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: [21, 33, 55, 77]
  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: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/tmp
  Threads: 16
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/spades.log


===== Read error correction started. 


== Running read error correction tool: /gpfs0/scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades-hammer /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info
  0:00:00.004     4M / 4M    INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.004     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.004     4M / 4M    INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.057     4M / 4M    INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.058     4M / 4M    INFO    General                 (hammer_tools.cpp          :  36)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.058     4M / 4M    INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.058     4M / 4M    INFO   K-mer Counting           (kmer_data.cpp             : 280)   Estimating k-mer count
  0:00:00.334   260M / 260M  INFO   K-mer Counting           (kmer_data.cpp             : 285)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
  0:06:06.950   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 294)   Processed 43334790 reads
  0:06:06.950   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 285)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
  0:12:37.626   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 294)   Processed 88493589 reads
  0:12:37.626   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 299)   Total 88493589 reads processed
  0:12:39.123   320M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 306)   Estimated 21912863491 distinct kmers
  0:12:39.125    64M / 320M  INFO   K-mer Counting           (kmer_data.cpp             : 311)   Filtering singleton k-mers
44 8 0
nslots: 68719476736
bits per slot: 8 range: 0000100000000000
  0:12:39.125    81G / 81G   INFO   K-mer Counting           (kmer_data.cpp             : 317)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
  2:31:31.587    81G / 81G   INFO   K-mer Counting           (kmer_data.cpp             : 326)   Processed 43334790 reads
  2:31:31.593    81G / 81G   INFO   K-mer Counting           (kmer_data.cpp             : 317)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
  4:49:11.327    81G / 81G   INFO   K-mer Counting           (kmer_data.cpp             : 326)   Processed 88493589 reads
  4:49:11.328    81G / 81G   INFO   K-mer Counting           (kmer_data.cpp             : 331)   Total 88493589 reads processed
  4:49:11.383    81G / 81G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  4:49:11.383    81G / 81G   INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  4:49:11.397    81G / 81G   INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 4224
  4:49:11.398    81G / 81G   INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 3.51807 Gb
  4:49:11.398    81G / 81G   INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 262144
  4:53:08.802    89G / 89G   INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R1.normalised.fastq
  4:56:01.077    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 5011320 reads
  4:57:07.415    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 9116411 reads
  4:58:10.764    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 13645695 reads
  4:59:25.548    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 17907661 reads
  5:00:28.031    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 22229606 reads
  5:01:36.956    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 26788200 reads
  5:02:41.890    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 31331777 reads
  5:04:21.561    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 36002288 reads
  5:05:49.361    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 40579473 reads
  5:06:34.607    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 43334790 reads
  5:06:34.607    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             :  97)   Processing /gpfs0/scratch/shiming/trimmed_sequences/fastq/CFC280618_S3_R2.normalised.fastq
  5:07:54.456    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 48404389 reads
  5:13:26.306    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 107)   Processed 67817903 reads
  5:18:38.920    89G / 90G   INFO   K-mer Splitting          (kmer_data.cpp             : 112)   Total 88493589 reads processed
  5:18:44.154    81G / 90G   INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  5:28:04.207    81G / 90G   INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 5845832720 kmers in total.
  5:28:04.207    81G / 90G   INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  5:32:39.909    81G / 90G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  5:44:19.128    83G / 90G   INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  5:45:52.933    83G / 90G   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 2710741562 bytes occupied (3.70964 bits per kmer).
  5:45:53.698     2G / 90G   INFO   K-mer Counting           (kmer_data.cpp             : 356)   Arranging kmers in hash map order
  8:40:07.610    89G / 90G   INFO    General                 (main.cpp                  : 148)   Clustering Hamming graph.
 12:16:01.420    89G / 90G   INFO    General                 (main.cpp                  : 155)   Extracting clusters


== Error ==  system call for: "['/gpfs0/scratch/shiming/tools/SPAdes-3.13.0-Linux/bin/spades-hammer', '/gpfs0/scratch/shiming/trimmed_sequences/fastq/Assembly-Spades/CFC280618_metaspades/corrected/configs/config.info']" finished abnormally, err code: -9

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.

Will anyone be kind enough to advice on how to resolve this?

Thank You

assembly
• 3,574 views • link
updated by Sej Modha Sej Modha • written by Ming • Ming

1 answer

It has been reported as a RAM related issue on the SPAdes github page, try and specify RAM with --memory option and see if that helps.

• 0 views • link
written by Sej Modha Sej Modha

Thank you very much!

• 0 views • link
written by Ming • Ming

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