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  1. UGENE
  2. UGENE-725

Can't load BAM file from remote source mounted to file system

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.10.2, 1.11
    • Component/s: None
    • Labels:

      Description

      The bug reported by UGENE paper reviewer:

      Use case: Try to view one of the 1000 Genomes project BAM files directly from the FTP site, e.g. 13GB file:
      ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam

      1. New UGENE project
      2. Try add existing file, no - that browses the file system
      3. Try menu "File", "Access remote database", no - that is things like GenBank and UniProt
      4. Try menu "Tools", "Import BAM/SAM file", no - that too browses the file system.
      5. Be clever and in Mac OS Finder first connect to the FTP server so it is listed under /Volumes
      6. Right click on project pane to add BAM file, select remote file via the file system mounting of the FTP site
      7. Contig table appears, listing chromosome etc (84 contigs in total)
      8. Press import, fails. Notice it seems to want to write the UGENE file to the FTP site!
      7. Try again, but this time edit the import path to a local path, e.g. /tmp/test_HG000096.bam.ugenedb but it still failed:

      [ERROR][12:18] Task

      {Loading documents}

      finished with error: Subtask

      {Opening view for document: HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam}

      is failed: Subtask

      {Adding document to project: HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam}

      is failed: Subtask

      {BAM/SAM file import: HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam}

      is failed: Subtask

      {Convert BAM to UGENE database (test_HG000096.bam.ugenedb)}

      is failed: Converting assembly from HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam to test_HG000096.bam.ugenedb failed: Can't decompress dataDocument was removed

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            Assignee:
            inovikov Ivan Novikov
            Reporter:
            iefremov Ivan Efremov
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              Dates

              Created:
              Updated:
              Resolved: