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  • In search of a sign in the data: When is a HiSeq run really done?

    A maybe odd, but interesting question: Is there an easy way to see, if a HiSeq run has finished producing data, if you are not able to take a look at the HiSeq itself and its display? I mean, I would like to just look at the data it produced on our cluster and say: Hey, this run is done, because there exists a file called "run_finsihed_successfully.txt" in the run folder or something like it. Does somebody know an answer to this?

  • #2
    Yes.

    This is with a GAIIx, not a high-seq, but I have the following files appearing:
    Basecalling_Netcopy_complete.txt

    Depending of what information you want, this might also be of interest:
    ImageAnalysis_Netcopy_complete.txt

    You also have a similar file for each of the reads also.

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    • #3
      For the GAII fpepin is right, the Basecalling_Netcopy_complete_SINGLEREAD.txt or Basecalling_Netcopy_complete_READ2.txt files signal the end of the run. These are generated only when a single or paired end run is finished producing data.

      For the HiSeq, parse the RunInfo.xml file to determine the number of expected reads and then look for the corresponding Basecalling_Netcopy_complete_Read*.txt file. Here is the python code to handle both of these cases:

      https://github.com/chapmanb/bcbb/blo...ed_msg.py#L179

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      • #4
        Thanks a lot for the information (and the code!) fpepin and Brad-Chapman.

        I suppose it is a bug, that "Basecalling_Netcopy_complete.txt" is created after the first read already and not (logically) after the last one, but I can live with that.

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