Error: Attribute names can't start with sys_ or contain characters besides letters, numbers, spaces, dashes or underscores

Post author
Tiffany Miller

Hello, I am trying to upload the following sample.tsv in a Terra on Azure workspace. Note: it is utilizing gs:// paths that I plan to update.

I am getting this error and I can't figure out what in the file is causing the issue: Attribute names can't start with sys_ or contain characters besides letters, numbers, spaces, dashes or underscores. 

The full error

{ "timestamp": "2023-11-16T16:37:21.868+00:00", "status": 400, "error": "Bad Request", "message": "Attribute names can't start with sys_ or contain characters besides letters, numbers, spaces, dashes or underscores.", "path": "/1996f47d-f2fd-4acb-a5d8-b09899753c96/tsv/v0.2/sample" }

Txt version of file:

entity:sample_id    analysis_ready_bam    cram    fastq1    fastq2    fastq_interleaved    library_name    participant    platform_name    platform_unit    read_group    run_date    sequencing_center
NA12878_small    gs://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_small.hg38.bam    gs://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram    gs://gatk-test-data/wgs_fastq/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq    gs://gatk-test-data/wgs_fastq/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_2.fastq    gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq    Solexa-NA12878    {"entityType":"participant","entityName":"NA12878"}    illumina    H06HDADXX130110.1.ATCACGAT    NA12878_A    2016-09-01T02:00:00+0200    BI

Can you help identify the error? Can I request a feature to make the error more useful by identifying the line(s) causing the issues?

Note: I tried removing the columns with the { } and the + and still had issues uploading. 

Thank you!

Comments

5 comments

  • Comment author
    Josh Evans

    Hi Tiffany,

    Thanks for writing in! I'm having difficulty replicating the error that you're currently seeing.  I have a few follow up questions that should help me troubleshoot this issue:

    • Can we have a copy of the exact TSV file that you're seeing the issue with? 
    • What application was used to create this file?
    • Was data copy and pasted into this file? So from which application was it copied from? (i.e. word document, Google Sheets, ect.) 

    Please let me know the answers to those questions and we'll take a look as soon as we can.

    Best,

    Josh

    0
  • Comment author
    Tiffany Miller

    Hi Josh, I can email the tsv to you. I downloaded the tsv from a Terra workspace and then edited it in MS Excel. 

    0
  • Comment author
    Josh Evans

    Hi Tiffany,

    Thanks for providing that information.  I did some testing with your files and I believe that I have a possible solution.  The files that you provided have the first column listed as entity:sample_id.  As it turns out, tsv files for Terra on Azure shouldn't use the entity: label as with Terra on GCP.

    I changed the column to sample_id and the file uploaded correctly.

    Please give that a try and let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Tiffany Miller

    Hi Josh, I had a hunch that was it. This thread will hopefully help others who hit this error message. 

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  • Comment author
    Josh Evans

    Hi Tiffany,

    Thanks for the reply! I'm glad I could help.

    Best,

    Josh

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