Question: Spades error code 6
0
gravatar for imdad.ce07buet
2.7 years ago by
imdad.ce07buet0 wrote:

I ran the folowing command for assembly in Spades and having the error:

/home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades.py -1 14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq -2 147
77x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq -s 14777x5_singletons_merged.fastq --meta -o 14777x5_assembly1 -t 32 -m 300 &

Command line: /home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades.py    -1  /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq -2  /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq -s  /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_singletons_merged.fastq    --meta  -o  /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1  -t  32  -m  300 

System information:
  SPAdes version: 3.11.1
  Python version: 2.7.5
  OS: Linux-3.10.0-514.6.1.el7.x86_64-x86_64-with-centos-7.3.1611-Core

Output dir: /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1
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: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R1_001_prinseq_good_rHpg.fastq']
      right reads: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_S1_L001_R2_001_prinseq_good_Yy8G.fastq']
      interlaced reads: not specified
      single reads: ['/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_singletons_merged.fastq']
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed (with gzip)
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: /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/tmp
  Threads: 32
  Memory limit (in Gb): 300

=== Stack Trace ===
[0x40c26a]
[0x6805d0]
[0x7a3989]
[0x7ac52d]
[0x7ee5d9]
Verification of expression 'f' failed in function 'void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]'. In file '/spades/src/common/utils/kmer_mph/kmer_splitters.hpp' on line 126. Message 'Cannot open temporary file to write'.
Verification of expression 'f' failed in function 'void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]'. In file '/spades/src/common/utils/kmer_mph/kmer_splitters.hpp' on line 126. Message 'Cannot open temporary file to write'.
spades: /spades/src/common/utils/kmer_mph/kmer_splitters.hpp:126: void utils::KMerSortingSplitter<Seq>::DumpBuffers(const files_t&) [with Seq = RuntimeSeq<128ul>; fs::files_t = std::vector<std::basic_string<char> >]: Assertion `f' failed.


== Error ==  system call for: "['/home/mdimdadi/Downloads/SPAdes-3.11.1-Linux/bin/spades', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/config.info', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/mda_mode.info', '/home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/K21/configs/meta_mode.info']" finished abnormally, err code: -6

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.
assembly • 1.8k views
ADD COMMENTlink modified 2.7 years ago by genomax91k • written 2.7 years ago by imdad.ce07buet0

Cannot open temporary file to write

I would start there and debug. Looks like you can't write to /home/mdimdadi/14777R/FastQ/Passed_Reads/14777x5/14777x5_assembly1/ this directory from the account you are using to run SPAdes.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax91k
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