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  1. UGENE
  2. UGENE-7251

Crash in bam_sort.c:409

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Cannot Reproduce
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
    • Sprint:
      DEV-40-2, DEV-40-3, DEV-40-4, DEV-40-5, DEV-40-RELEASE, DEV-41-1, DEV-41-2, DEV-41-3, DEV-41-4, DEV-41-5, DEV-41-RELEASE, DEV-42-1, DEV-42-2, DEV-42-3, DEV-42-4, DEV-42-5, DEV-42-RELEASE, DEV-43-1, DEV-47-1, DEV-47-2, DEV-47-3, DEV-47-4, DEV-47-5, DEV-47-RELEASE, DEV-48-1, DEV-48-2, DEV-48-3, DEV-48-4, DEV-48-5, DEV-48-RELEASE, DEV-49-1, DEV-49-2, DEV-49-3, DEV-49-4, DEV-49-5, DEV-49-RELEASE, DEV-50-1, DEV-50-2, DEV-50-3, DEV-50-4, DEV-50-5
    • Affect Type:
      Userdefined

      Description

      Crash reports 821, 827, 829, 831, 842.

      Presumably, the reason for the crash is as follows. The user has 3 GB of RAM. In line bam_sort.c:406, C-style memory allocation is performed, which is not checked for zero.

      samtools is an external tool, its current version is very different from that used in UGENE.

      I analyzed crash report 831 and made the following scenario:

      1. Tools->NGS data analysis->Map reads to reference...
      2. Select BWA-SW Mapping tool.
      3. Set "_common_data/scenarios/_regression/7251/ref Paracheirodon axelrodi.fas" as Reference.
      4. Set "Protocheirodon pi cons2.sam" as Result file name.
      5. Add "_common_data/scenarios/_regression/7251/Protocheirodon pi sra_data.fastq(23).gz" as Reads.
      6. Set -b, -q, -r parameters to 1.
      7. Click Start.
      8. Repeat previous steps for the same reference and "Compsura heterura sra_data.fastq(25).gz".
      9. Wait for "Import SAM file" dialogs (~15--30 min).
      10. Click "Import" x2.

      On my computer (32 GB of RAM) the problem did not reproduce. It is required to discuss the correctness of the problem and how to solve it.

        Attachments

          Issue Links

          is blocked by

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-7057 Upgrade built-in samtools package in UGENE

          • Major - Major loss of function.
          • Closed
          is duplicated by

          Bug - A problem which impairs or prevents the functions of the product. UGENE-7566 Check memory allocation in bam_index.c

          • Major - Major loss of function.
          • Closed
          relates to

          Bug - A problem which impairs or prevents the functions of the product. UGENE-7672 [NGS] Crash cancel bwa

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. UGENE-7566 Check memory allocation in bam_index.c

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              yalgaer Yuliya Algaer
              Reporter:
              biserova Evelina
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: