Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Import raw data to SMRTLink

    I find raw data (bam file, subread.xml..) from Pacbio. I added to SMRTLink. but when I use this data to assembly by HAGP4, SMRTLink noticed fail.
    Can I help me how to add raw data to SMRTLink?
    P/s: We have a Pacbio SQUEL.

    This is log file when i add subread file to SMRTLink.
    [INFO] [2018-01-29T21:37:05.659-05:00] Running job-type import_dataset com.pacbio.secondary.analysis.jobtypes.ImportDataSetJob@42d380d9 in /opt/pacbio/smrtlink/userdata/jobs_root/000/000037
    [INFO] [2018-01-29T21:37:06.440-05:00] Can't process this dataset
    [INFO] [2018-01-29T21:37:06.485-05:00] Completed running job import_dataset Result -> Success(Right(PacBioDataStore(2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,0.2.1,List(DataStoreFile(36c19ac0-c34b-fc6b-86f2-743a3da771e3,pbscala::import_dataset,PacBio.DataSet.SubreadSet,2410,2018-01-29T21:37:05.659-05:00,2018-01-29T21:37:05.659-05:00,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,false,pacbio_dataset_subreadset-160923_085639252,Imported DataSet on 2018-01-29T21:37:05.659-05:00), DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job), DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report)))))
    [INFO] [2018-01-29T21:37:06.485-05:00] attempting to import
    PacBioDataStore Summary 3 files Created at 2018-01-29T21:37:06.485-05:00 Schema version 0.2.1
    1. DataStoreFile(36c19ac0-c34b-fc6b-86f2-743a3da771e3,pbscala::import_dataset,PacBio.DataSet.SubreadSet,2410,2018-01-29T21:37:05.659-05:00,2018-01-29T21:37:05.659-05:00,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,false,pacbio_dataset_subreadset-160923_085639252,Imported DataSet on 2018-01-29T21:37:05.659-05:00)
    2. DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job)
    3. DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report)
    [INFO] [2018-01-29T21:37:06.568-05:00] Successfully inserted datastore files:
    [INFO] [2018-01-29T21:37:06.568-05:00] Successfully entered SubreadSet SubreadServiceDataSet(-99,36c19ac0-c34b-fc6b-86f2-743a3da771e3,pacbio_dataset_subreadset-160923_085639252,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,2018-01-29T21:37:06.544-05:00,2018-01-29T21:37:06.544-05:00,573889,5347463396,3.0.1, ,subreadset,9a6026d88580d6130acbbe2d28e98c55,54113,m54113_160914_092411,PacBio_LER0_32kbLibrary_1_3_C01,3_C01,unknown,0,PacBio_LER0_32kbLibrary_1_3_C01,None,37,1,PacBio.DataSet.SubreadSet)
    Unsupported DataSet type PacBio.FileTypes.log. Imported DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job). Skipping extended/detailed importing
    Unsupported DataSet type PacBio.FileTypes.JsonReport. Imported DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report). Skipping extended/detailed importing

  • #2
    For a quick resolution, file a ticket with Pacbio tech support.

    Alternatively, what version of SMRT Link are you using, and where did the data come from?

    Comment


    • #3
      Originally posted by rhall View Post
      For a quick resolution, file a ticket with Pacbio tech support.

      Alternatively, what version of SMRT Link are you using, and where did the data come from?
      SMRT Link version is 5.01
      I get data from pacbio: https://www.pacb.com/blog/sequel-sys...nome-assembly/

      Comment


      • #4
        Can you try on the command line
        Code:
        pbservice import-dataset --host <hostname> --port <port> m54113_160914_092411.subreadset.xml --verbose

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X