BCL converter error

[vebaev]

Hi all,

I'm trying to get the fast file from our demo PhiX run and I have some error in the nohup.out after make -j command

here is the output - http://pastebin.com/x0VT9vEx

so I got empty fastq.gz files

[GenoMax]

Here are the clues from your error log. At least two BCL files are missing from your data set.

File /mnt/storage/DATA/GAIIX/Data/Intensities/BaseCalls/L006/C1.1/s_6_1.bcl does not exist

File /mnt/storage/DATA/GAIIX/Data/Intensities/BaseCalls/L008/C31.1/s_8_1.bcl does not exist

To get around this problem you can use the "--ignore-missing-bcl" command line option for configureBclToFastq. This will interpret missing *.bcl files as no call.

[vebaev]

Thanks!

I also noticed:


Error: 2012-Nov-16 14:48:07: No such file or directory: /home/milev/CASAVA_v1.8.2/src/c++/lib/alignment/BclReader.cpp(86): Throw in function unsigned int casava::alignment::BclReader::readClusterCount()