Software  ›   pipelines
If your question is not answered here, please email us at:  ${email.software} # 10x GenomicsChromium De Novo Assembly # Troubleshooting Supernova If the supernova demux or supernova run pipelines fail, they will automatically generate a "debug tarball" that contains the logs and metadata generated by the pipestance leading up to failure. This file, named sampleid.mri.tgz, can be e-mailed to the 10x software team to help resolve any issues with using Supernova. You may also use the supernova upload command to send the tarball to 10x: $ supernova upload [email protected] sample_id.mri.tgz


If you wish to troubleshoot a pipeline failure yourself, it is important to identify if you are experiencing a preflight failure, an in-flight failure, or an alert.

## Preflight Failures

Preflight failures are the most common and are the result of invalid input data or runtime parameters. Because they occur before the pipeline actually runs, there will be no pipeline output and the error is reported directly to your terminal.

supernova demux will generate the following error if Illumina's bcl2fastq software is not installed:

[error] bcl2fastq or configureBclToFastq.pl not found on PATH on workstation.university.edu.

## In-Flight Failures

In-flight failures may be the result of factors external to the pipeline such as running out of system memory or disk space, or may be due to issues with the data that could not be detected prior to de novo assembly. Different stages may fail in different ways, so the specific error messages vary widely.

### Finding relevant error logs

There are a few important files that are saved to your pipeline output directory which, by default, is named according to the flowcell serial number for supernova demux (e.g., HAWT7ADXX) and your --id name for supernova run.

1. The pipeline execution log that is output to your terminal during pipeline execution is also saved to output_dir/_log.

2. Stages that experience a hard failure generate an _errors file containing the precise error that caused a stage to halt. You view these error logs, if they exist, using find output_dir -name _errors | xargs cat

3. Each stage also logs its stdout and stderr streams to _stderr and _stdout files. These logs can be listed using find output_dir -name _stderr and may contain elucidating error messages in stages that execute third-party applications such as BWA and GATK.

A more detailed description of the pipeline output directory and its contents is given in the Pipestance Structure page.

### Resuming a failed pipestance

Once you have determined the reason for failure and are ready to continue running the pipeline, you can typically issue the same supernova run or supernova demux command to continue execution of the pipestance from the stage that originally failed.

When supernova run or supernova demux is run, it will detect if its intended output directory already exists. If it does, this existing pipeline output directory will be treated as an incomplete pipestance and resume execution. This feature allows pipelines to be stopped and resumed with great flexibility, but it can also result in errors such as:

RuntimeError: /home/jdoe/runs/sample345 is not a pipestance directory

which indicates that you specified a --id that corresponds to an existing directory that was not created by supernova run.

The following error:

RuntimeError: pipestance 'HAWT7ADXX' already exists and is locked by another Martian instance. If you are sure no other Martian instance is running, delete the _lock file in /home/jdoe/runs/HAWT7ADXX and start Martian again.

indicates that you may already have a copy of supernova run or supernova demux running that is using the same output directory. If you are sure that there is no pipestance running in the given output directory, you can either remove that output directory entirely (mv HAWT7ADXX HAWT7ADXX.old) to restart the pipestance from the beginning, or you can remove the pipestance's lock file (rm HAWT7ADXX/_lock) and re-run the supernova run command to resume pipeline execution.

If you encounter the following error when attempting to resume a pipestance:

RuntimeError: pipestance 'sample345' already exists with different invocation file /home/jdoe/runs/sample345/_invocation

you are attempting to resume a pipestance using command-line arguments that are different from those used to first run it. You can view the parameters input to the existing pipeline by examining the _log file located in the output directory (e.g., head -n20 /home/jdoe/runs/sample345/_log)

Alerts:
We observe many reads shorter than 150 bases.The ideal read length for Supernova is 150 bases. Reads shorter than the ideal length are likely to yield a lower quality assembly.
[error] The fraction of input reads having valid barcodes is 20.3 percent, whereas the ideal is at least 80 percent. This condition could have multiple causes including wrong library type, failed library construction and low sequence quality on the barcode bases. This could have a severe effect on assembly performance, and Supernova has not been tested on data with these properties, so execution will be terminated.