BCL to FASTQ conversion error

[tahamasoodi]

I am using CASAVA 1.8.2 on a separate machine and trying to convert bcl files generated by Hiseq 2000 to fastq but I am getting an error message that config.xml file does not exist at /usr/local/lib/CASAVA-1.8.2/perl/Casava/Demultiplex.pm line 111.
Can anyone please help me out from this issue.
Thanks

[seb567]

I think it may be trying to use a XML file as the sample sheet for demultiplexing your data.
Did you provide --sample-sheet ?

See https://github.com/sebhtml/FastDemul...with-CASAVA.sh
for an example.


Sébastien Boisvert

I am using CASAVA 1.8.2 on a separate machine and trying to convert bcl files generated by Hiseq 2000 to fastq but I am getting an error message that config.xml file does not exist at /usr/local/lib/CASAVA-1.8.2/perl/Casava/Demultiplex.pm line 111.
Can anyone please help me out from this issue.
Thanks

[tahamasoodi]

Error in bcl to fastq

Thanks seb567, no I don't have a sample-sheet. I just want to convert bcl to fastq.

[seb567]

In your run directory, you should have these files:


./Data/Intensities/BaseCalls/config.xml
./Data/Intensities/config.xml


I think they are missing in your case.