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Troubleshooting guide

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Here are a few troubleshooting tips for some of the common issues that you might face when using the Microsoft Genomics service, MSGEN.

For FAQ, not related to troubleshooting, see Common questions.

Step 1: Locate error codes associated with the workflow

You can locate the error messages associated with the workflow by:

  1. Using the command line and typing in msgen status
  2. Examining the contents of standardoutput.txt.

1. Using the command line msgen status

msgen status -u URL -k KEY -w ID

There are three required arguments:

  • URL - the base URI for the API

  • KEY - the access key for your Genomics account

    • To find your URL and KEY, go to Azure portal and open your Microsoft Genomics account page. Under the Management heading, choose Access keys. There, you find both the API URL and your access keys.

  • ID - the workflow ID

    • To find your workflow ID type in msgen list command. Assuming your config file contains the URL and your access keys, and is located is in the same location as your msgen exe, the command will look like this:

      msgen list -f "config.txt"

      Output from this command will look like this :

          Microsoft Genomics command-line client v0.7.4
        Copyright (c) 2018 Microsoft. All rights reserved.

        Workflow List
        -------------
        Total Count  : 1

        Workflow ID     : 10001
        Status          : Completed successfully
        Message         :
        Process         : snapgatk-20180730_1
        Description     :
        Created Date    : Mon, 27 Aug 2018 20:27:24 GMT
        End Date        : Mon, 27 Aug 2018 20:55:12 GMT
        Wall Clock Time : 0h 27m 48s
        Bases Processed : 1,348,613,600 (1 GBase)

    Note

    Alternatively you can include the path to the config file instead of directly entering the URL and KEY. If you include these arguments in the command line as well as the config file, the command-line arguments will take precedence.

For workflow ID 1001, and config.txt file placed in the same path as the msgen executable, the command will look like this:

msgen status -w 1001 -f "config.txt"

2. Examine the contents of standardoutput.txt

Locate the output container for the workflow in question. MSGEN creates a, [workflowfilename].logs.zip folder after every workflow execution. Unzip the folder to view its contents:

  • outputFileList.txt - a list of the output files produced during the workflow
  • standarderror.txt - this file is blank.
  • standardoutput.txt - logs all top-level status messages including errors, that occurred while running the workflow.
  • GATK log files - all other files in the logs folder

For troubleshooting, examine the contents of standardoutput.txt and note any error messages that appear.

This section briefly highlights common errors output by Microsoft Genomics service (msgen) and the strategies you can use to resolve them.

The Microsoft Genomics service (msgen) can throw the following two kinds of errors:

  1. Internal Service Errors: Errors that are internal to the service, that may not be resolved by fixing parameters or input files. Sometimes resubmitting the workflow might fix these errors.
  2. Input Errors: Errors that can be resolved by using the correct arguments or fixing file formats.

1. Internal service errors

An Internal service error is not user actionable. You may resubmit the workflow but if that does not work, contact Microsoft Genomics support

Error message Recommended troubleshooting steps
An internal error occurred. Try resubmitting the workflow. If you see this error again, contact Microsoft Genomics support for assistance Submit the workflow again. Contact Microsoft Genomics support for assistance if the issue persists by creating a support ticket.

2. Input errors

These errors are user actionable. Based on the type of file, and error code, Microsoft Genomics service outputs distinct error codes. Follow the recommended troubleshooting steps listed below.

Type of file Error code Error message Recommended troubleshooting steps
Any 701 Read [readId] has [numberOfBases] bases, but the limit is [maxReadLength] The most common reason for this error is file corruption leading to concatenation of two reads. Check your input files.
BAM 200 Unable to read file '[yourFileName]'. Check the format of the BAM file. Submit the workflow again with a properly formatted file.
BAM 201 Unable to read BAM file [File_name]. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 202 Unable to read BAM file [File_name]. File too small and missing header. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 203 Unable to read BAM file [File_name]. Header of file was corrupt. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 204 Unable to read BAM file [File_name]. Header of file was corrupt. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 205 Unable to read BAM file [File_name]. Header of file was corrupt. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 206 Unable to read BAM file [File_name]. Header of file was corrupt. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 207 Unable to read BAM file [File_name]. File truncated near offset [offset]. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
BAM 208 Invalid BAM file. The ReadID [Read_Id] has no sequence in file [File_name]. Check the format of the BAM file. Submit the workflow with a correctly formatted file.
FASTQ 300 Unable to read FASTQ file. [File_name] doesn't end with a newline. Correct the format of the FASTQ file and submit the workflow again.
FASTQ 301 Unable to read FASTQ file [File_name]. FASTQ record is larger than buffer size at offset: [_offset] Correct the format of the FASTQ file and submit the workflow again.
FASTQ 302 FASTQ Syntax error. File [File_name] has a blank line. Correct the format of the FASTQ file and submit the workflow again.
FASTQ 303 FASTQ Syntax error. File[File_name] has an invalid starting character at offset: [_offset], line type: [line_type], character: [_char] Correct the format of the FASTQ file and submit the workflow again.
FASTQ 304 FASTQ Syntax error at readID [_ReadID]. First read of batch doesn’t have readID ending in /1 in file [File_name] Correct the format of the FASTQ file and submit the workflow again.
FASTQ 305 FASTQ Syntax error at readID [_readID]. Second read of batch doesn’t have readID ending in /2 in file [File_name] Correct the format of the FASTQ file and submit the workflow again.
FASTQ 306 FASTQ Syntax error at readID [_ReadID]. First read of pair doesn’t have an ID that ends in /1 in file [File_name] Correct the format of the FASTQ file and submit the workflow again.
FASTQ 307 FASTQ Syntax error at readID [_ReadID]. ReadID doesn’t end with /1 or/2. File [File_name] can't be used as a paired FASTQ file. Correct the format of the FASTQ file and submit the workflow again.
FASTQ 308 FASTQ read error. Reads of both ends responded differently. Did you choose the correct FASTQ files? Correct the format of the FASTQ file and submit the workflow again.

Step 3: Contact Microsoft Genomics support

If you continue to have job failures, or if you have any other questions, contact Microsoft Genomics support from the Azure portal. Additional information on how to submit a support request can be found here.

Next steps

In this article, you learned how to troubleshoot and resolve common issues with the Microsoft Genomics service. For more information and more general FAQ, see Common questions.