bclToFastq conversion error

[a.kmg]

Hello to all,

I get some errors with the bclToFastq tool, of type:

[2014-12-17 14:41:54] [lame26] [Temp/L006_R1_demux_summary.xml] Error: 2014-Dec-17 14:41:54: Success: CASAVA_v1.8.2/src/c++/lib/alignment/BclReader.cpp(148): Throw in function void casava::alignment::BclReader::getCluster(std::string&, std::string&)
[2014-12-17 14:41:54] [lame26] [Temp/L006_R1_demux_summary.xml] Dynamic exception type: boost::exception_detail::clone_impl<casava::common::IoException>
[2014-12-17 14:41:54] [lame26] [Temp/L006_R1_demux_summary.xml] std::exception::what: Failed to read BCL file Data/Intensities/BaseCalls/L006/C53.1/s_6_1107.bcl.
[2014-12-17 14:41:54] [lame26] [Temp/L006_R1_demux_summary.xml] : Failed to read BCL file Data/Intensities/BaseCalls/L006/C53.1/s_6_1107.bcl.
make: *** [Temp/L006_R1_demux_summary.xml] Error 1

But when I do, for example:

ls Data/Intensities/BaseCalls/L006/C53.1/s_6_1107.bcl

The file exists.

Someone has already encountered this problem? My bcl file has not been modified, it comes directly from Illumina sequencer. On the sequencer, the data are of good quality and have been correctly demultiplexed. As I understand it, the getCluster function is empty, yet my file is not empty ...

I have never encountered this problem. My samples are multiplexed on multiple lanes, so the bcltofastq tool must pool them. Yet I have done this several times, no problem. To make the samples pool, the bcltofastq tool is based on sample names in the samplesheet?

Thanks in advance.

[GenoMax]

If the files exists can you check to see if there is a read permission problem? Have you checked to see if the file zero bytes in size? If that is the case then you will need to add --ignore-missing-bcl option to your ConfigureFastqToBcl.pl command line.

[a.kmg]

Thank you for your reply.

Yes I can read this file, the size is different of 0 and I tried with the --ignore-missing-bcl option but I get the same error ... that's why I really do not understand the issue.

EDIT : I just run the command by not taking into account the tiles that generate an error (there are 12!). I'll see if this solves my problem.

EDIT 2 :

Now I get

[2014-12-17 16:21:17] [lame26] [Temp/L006_R1_demux_summary.xml] Error: 2014-Dec-17 16:21:17: Success: /CASAVA_v1.8.2/src/c++/lib/alignment/BclReader.cpp(272): Throw in function virtual unsigned int casava::alignment::FiltersReaderImpl_16bits::doGetNextFilter(std::istream&)
[2014-12-17 16:21:17] [lame26] [Temp/L006_R1_demux_summary.xml] Dynamic exception type: boost::exception_detail::clone_impl<casava::common::IoException>
[2014-12-17 16:21:17] [lame26] [Temp/L006_R1_demux_summary.xml] std::exception::what: Failed to read filter value.
[2014-12-17 16:21:17] [lame26] [Temp/L006_R1_demux_summary.xml] [casava::alignment::tag_errmsg*] = Fileata/Intensities/BaseCalls/L006/s_6_1109.control Cluster: 3145723
[2014-12-17 16:21:17] [lame26] [Temp/L006_R1_demux_summary.xml] : Failed to read filter value.
make: *** [Temp/L006_R1_demux_summary.xml] Error 1

And I get the same errors that before, but on others tiles ... very strange.

[a.kmg]

I write here the solution of my problem.

Some of my files have been corrupted during the transfer of these files from sequencer to my server.

To ignore this corrupted files, the tech support of Illumina give me this solution:

1) rename the corrupted files from .bcl to .bclOFF and use the "--ignore-missing-bcl --ignore-missing-control --ignore-missing-stats" parameters in the bclToFastq command of Casava

2) navigate to the config.xml in the Basecalls directory. Edit in notepad, removing the line containing the corrupt tiles from the relevant lane.


For example, the file Data/Intensities/BaseCalls/L006/C53.1/s_6_1107.bcl was corrupted, so :

1) I renamed the file : Data/Intensities/BaseCalls/L006/C53.1/s_6_1107.bclOFF

2) I remove the tile "1107" of lane 6 in config.xml

And it works fine !