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  1. UGENE
  2. UGENE-4222

Investigate NGS data de novo assembling

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: 1.16.1
    • Fix Version/s: None
    • Component/s: NGS
    • Story Points:
      13
    • Sprint:
      DEV-06/05/2015
    • Affect Type:
      Userdefined

      Description

      FASTQ files can be successfully assembled using CLC bio, but SPAdes returned an error (on the same computer).

      I have change source fastq files (different phage) and after successful assembly using clc I tried to do the same with spades,
      log below:
      Quote:
      [ERROR][11:11] Spades: == Error == system call for: "['/Volumes/Unipro UGENE 1.16.0/Unipro UGENE.app/Contents/MacOS/tools/SPAdes-3.1.1/bin/hammer', '/Biofizyka/UGENE/Bakteriofagi/JD/ZK1_01/corrected/configs/config.info']" finished abnormally, err code: -6
      [ERROR][11:11] == Error == system call for: "['/Volumes/Unipro UGENE 1.16.0/Unipro UGENE.app/Contents/MacOS/tools/SPAdes-3.1.1/bin/hammer', '/Biofizyka/UGENE/Bakteriofagi/JD/ZK1_01/corrected/configs/config.info']" finished abnormally, err code: -6
      [ERROR][11:12] Task

      Unknown macro: {GenomeAssemblyMultiTask}

      finished with error: Subtask

      Unknown macro: {GenomeAssemblyTask}

      is failed: Subtask

      Unknown macro: {SPAdes tool}

      is failed: SPAdes tool exited with code 1

      Investigate other de novo assemblers for the data. For example:

      • SOAPdenovo
      • MIRA

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              Assignee:
              Unassigned
              Reporter:
              oigl Olga Golosova
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                Dates

                Created:
                Updated:
                Resolved: