Question: SPAdes assembler-Error code 255
gravatar for Menia_gavr
2.3 years ago by
Menia_gavr0 wrote:

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/ -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
    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/

   0:00:00.000    4M /    4M   INFO  General                 (main.cpp                  :  82)   Loading config from /home/gavri003/B9_Assembly/corrected/configs/
   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/']" finished abnormally, err code: 255

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

Thanks a lot! Menia

ADD COMMENTlink written 2.3 years ago by Menia_gavr0
gravatar for genomax
2.3 years ago by
United States
genomax87k wrote:

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.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by genomax87k

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 :)

ADD REPLYlink written 2.3 years ago by Menia_gavr0
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