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Illumina BaseSpace File System

I have tried to perform base calling using bcl on my own with bcl2fastq. Surprisingly I managed to install it, but I cant run since I get a following error:

ERROR: /tmp/basemount.mi.28931/Runs/

9491489/bsfs/data/Data/Intensities/BaseCalls/config.xml: file does not exist
    at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex.pm line 116

As written in guide, in Basecall folder should be config.xml file. But I don't have it! Moreover, I don't have config.xml in any other folder of the Run, not only in the Basecall folder. I've looked at other previous Runs, where bcl2fastq conversion was done automatically by Miseq without my intervention and I also haven't found any config.xml files. So how can I perform bcl2fastq conversion on my own and where should I search for config.xml?

next-gen-sequencing
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updated by Ram Ram • written by Max Ivon Max Ivon

What do you hope to achieve by doing your own basecalling when it sounds like you normally use the software on MiSeq/BaseSpace. I am not sure why you don't have config.xml files in any of your run folders.

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written by GenoMax GenoMax

Normally i have my own runs on my own machine. This time my college has shared run with me without project, so i dont have any access to data processing

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written by Max Ivon Max Ivon

2 answers

Hello M4merg,

Please can you tell me which Hiseq machine data you are using..? Is it Hi-Seq-4000 or below version..?

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updated by Ram Ram • written by BioRyder BioRyder

It appears to be a MiSeq based on the text from original post.

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written by GenoMax GenoMax

Yes, MiSeq was used

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written by Max Ivon Max Ivon

Processing of MiSeq data requires a specific version of Bcl2fastq software, namely version 2.17.

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written by KM • KM

That is not correct. One can use bcl2fastq v.1.8.4. On other hand NextSeq requires the new series v.2.x.

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written by GenoMax GenoMax

Only early versions of MiSeq - running RTA versions earlier than 1.8. Any newer MiSeq instrument needs Bcl2fastq version 2 to process data.

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updated by Ram Ram • written by KM • KM

Our MiSeq's have RTA 1.18.54 and we have not had any problems processing data offline with bcl2fastq v.1.8.4.

Do you have an official announcement/link?

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written by GenoMax GenoMax

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