Question: SPAdes assembler-Error code -6
0
gravatar for Menia_gavr
12 months ago by
Menia_gavr0
Menia_gavr0 wrote:

Hi guys,

I am new to bionformatics. I am trying to run my assembly with SPAdes and I get this error. I tried to decrease the RAM and threads that are occupied, but I still get the error. Any ideas?

Command line: /home/programs/assembly/SPAdes-3.0.0-Linux/bin/spades.py -1 B9_trimmed.1.fastq -2 B9_trimmed.2.fastq --careful -o /home/gavri003/B9_Assembly

System information:
  SPAdes version: 3.0.0
  Python version: 2.7.6
  OS: Linux-3.13.0-93-generic-x86_64-with-Ubuntu-14.04-trusty

Output dir: /home/gavri003/B9_Assembly
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/gavri003/B9_Assembly/B9_trimmed.1.fastq']
      right reads: ['/home/gavri003/B9_Assembly/B9_trimmed.2.fastq']
      interlaced reads: not specified
      single reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed (with gzip)
Assembly parameters:
  k: automatic selection based on read length
  MismatchCorrector will be used
  Repeat resolution is enabled
Other parameters:
  Dir for temp files: /home/gavri003/B9_Assembly/tmp
  Threads: 16
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /home/gavri003/B9_Assembly/spades.log


===== Read error correction started. 


== Running read error correction tool: /home/programs/assembly/SPAdes-3.0.0-Linux/bin/hammer /home/gavri003/B9_Assembly/corrected/configs/config.info

   0:00:00.000    4M /    4M   INFO  General                 (main.cpp                  :  82)   Loading config from /home/gavri003/B9_Assembly/corrected/configs/config.info
   0:00:00.001    4M /    4M   INFO  General                 (memory_limit.hpp          :  29)   Memory limit set to 250 Gb
   0:00:00.001    4M /    4M   INFO  General                 (main.cpp                  :  91)   Trying to determine PHRED offset
   0:00:00.001    4M /    4M   INFO  General                 (main.cpp                  :  97)   Determined value is 33
   0:00:00.002    4M /    4M   INFO  General                 (hammer_tools.cpp          :  49)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
     === ITERATION 0 begins ===
   0:00:00.002    4M /    4M   INFO K-mer Index Building     (kmer_index.hpp            : 467)   Building kmer index
   0:00:00.002    4M /    4M   INFO K-mer Splitting          (kmer_data.cpp             : 127)   Splitting kmer instances into 256 buckets. This might take a while.
   0:00:00.003    4M /    4M   INFO  General                 (file_limit.hpp            :  29)   Open file limit set to 1024
   0:00:00.003    4M /    4M   INFO K-mer Splitting          (kmer_data.cpp             : 150)   Memory available for splitting buffers: 5.20825 Gb
   0:00:00.003    4M /    4M   INFO K-mer Splitting          (kmer_data.cpp             : 159)   Using cell size of 262144
   0:00:43.883    8G /    9G   INFO K-mer Splitting          (kmer_data.cpp             : 181)   Processed 3315276 reads
   0:01:03.099    8G /    9G   INFO K-mer Splitting          (kmer_data.cpp             : 181)   Processed 4886811 reads
   0:01:47.794    8G /    9G   INFO K-mer Splitting          (kmer_data.cpp             : 181)   Processed 8340219 reads
   0:02:06.279    8G /    9G   INFO K-mer Splitting          (kmer_data.cpp             : 181)   Processed 9773622 reads
   0:02:06.281    8G /    9G   INFO K-mer Splitting          (kmer_data.cpp             : 186)   Processed 9773622 reads
   0:02:07.223   64M /    9G   INFO  General                 (kmer_index.hpp            : 345)   Starting k-mer counting.
   0:02:13.019   64M /    9G   INFO  General                 (kmer_index.hpp            : 351)   K-mer counting done. There are 186015006 kmers in total.
   0:02:13.020   64M /    9G   INFO  General                 (kmer_index.hpp            : 353)   Merging temporary buckets.
   0:02:15.173   64M /    9G   INFO K-mer Index Building     (kmer_index.hpp            : 476)   Building perfect hash indices
   0:02:57.154   68M /    9G   INFO  General                 (kmer_index.hpp            : 371)   Merging final buckets.
   0:03:10.101   68M /    9G   INFO K-mer Index Building     (kmer_index.hpp            : 515)   Index built. Total 64349595 bytes occupied (2.7675 bits per kmer).
   0:03:10.101   68M /    9G   INFO K-mer Counting           (kmer_data.cpp             : 267)   Arranging kmers in hash map order
   0:04:22.334   68M /    9G   INFO K-mer Counting           (kmer_data.cpp             : 280)   Done. Total swaps: 186014738
   0:04:23.129    1G /    9G   INFO  General                 (main.cpp                  : 151)   Clustering Hamming graph.
   0:04:23.129    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 115)   Serializing sub-kmers.
   0:04:23.129    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 120)   Serializing: [0, 10)
   0:05:53.899    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 120)   Serializing: [10, 21)
   0:07:24.190    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 129)   Splitting sub-kmers, pass 1.
   0:09:24.241    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 134)   Splitting done. Processed 2 blocks. Produced 5242482 blocks.
   0:09:24.241    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 145)   Merge sub-kmers, pass 1
   0:16:19.822    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 170)   Merge done, total 2249504 new blocks generated.
   0:16:20.228    1G /    9G   INFO Hamming Clustering       (hamcluster.cpp            : 175)   Spliting sub-kmers, pass 2.
=== Stack Trace ===
[0x4027fa]
[0x428065]
[0x4289f9]
[0x416533]
[0x55f110]
[0x4001b9]
hammer: /home/yasha/gitrep2/algorithmic-biology/assembler/src/hammer/hamcluster.cpp:54: std::pair<long unsigned int, long unsigned int> SubKMerSplitter::split(): Assertion `!ofs.fail()' failed.


== Error ==  system call for: "['/home/programs/assembly/SPAdes-3.0.0-Linux/bin/hammer', '/home/gavri003/B9_Assembly/corrected/configs/config.info']" finished abnormally, err code: -6

In case you have troubles running SPAdes, you can write to spades.support@bioinf.spbau.ru
Please provide us with params.txt and spades.log files from the output directory.

Thanks a lot! Menia

error -6 error spades assembler • 875 views
ADD COMMENTlink written 12 months ago by Menia_gavr0

I see that you are running an old version of SPAdes. It is currently in version 3.11.1. You may want to start by getting it upgraded to latest and see if the error goes away.

ADD REPLYlink written 12 months ago by genomax65k
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