SPAdes assembler-Error code 255

Question

[Menia_gavr]

Hi guys,

I am new to bioinformatics and I try to run my assembly with SPAdes but I get this 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
   0:00:00.002    4M /    4M  ERROR  General                 (main.cpp                  :  94)   Failed to determine offset! Specify it manually and restart, please!


== 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: 255

In case you have troubles running SPAdes, you can write to [e-mail]
Please provide us with params.txt and spades.log files from the output directory.

Thanks a lot! Menia

Answer 1

[GenoMax]

Failed to determine offset! Specify it manually and restart, please!

Try setting --phred-offset 33 or 64 manually and re-run. If you have recent sequence data then the offset will be 33 for sure.

How much RAM are you allocating to this job. Appears to be 250GB.

[Menia_gavr]

I set the offset at 33 and changed the memory to 50GB instead of 250GB...and it worked! Thanks a lot for the fast response :)