Configuration for long reads?

[MartinaFernandez]

Hi, how can I run the docker image to allow Long Nanopore reads? I tried

-e MODE=LONG

But the tool searchs for PE Illumina reads.

Thank you!

[michael-weinstein]

Let me check in on this. I have gotten this to work on long-reads before, but it's been a while. Can you show me your error messages?

[markus-soma]

Hi @michael-weinstein,

I am experiencing similar issues as @MartinaFernandez. We get the following error when using -e MODE=LONG:

Unable to find expected file for environment variable parameter reverseReads at /data/input/sequence/standard_submitted_R2.fastq
Traceback (most recent call last):
  File "/opt/miqscore16s/analyzeStandardReads.py", line 408, in <module>
    parameters = getApplicationParameters()
  File "/opt/miqscore16s/analyzeStandardReads.py", line 14, in getApplicationParameters
    parameters.addParameter("reverseReads", str, default=default.reverseReads, expectedFile=True)
  File "/opt/miqscore16s/miqScore16SPublicSupport/parameters/environmentParameterParser.py", line 393, in addParameter
    parameter = EnvVariable(name, typeRequirement, default, flag, validationList, lowerBound, upperBound, expectedFile, createdFile, expectedDirectory, createdDirectory, logLevel, required, externalValidation)
  File "/opt/miqscore16s/miqScore16SPublicSupport/parameters/environmentParameterParser.py", line 52, in __init__
    self.runValidations()
  File "/opt/miqscore16s/miqScore16SPublicSupport/parameters/environmentParameterParser.py", line 85, in runValidations
    self.validateExpectedFilePath()
  File "/opt/miqscore16s/miqScore16SPublicSupport/parameters/environmentParameterParser.py", line 121, in validateExpectedFilePath
    raise FileNotFoundError("Unable to find expected file %s" %self.value)
FileNotFoundError: Unable to find expected file /data/input/sequence/standard_submitted_R2.fastq

How can we run this tool on our Nanopore reads? Thanks!