bcl2fastq error? (bcl2fastq::common::InputDataError)

Question

[mhmtgenc85]

Hi everyone,

We have NextSeq 500 instrument that we used to sequence our samples. And as you know we get bcl files and need to use bcl2fastq to convert images to fastq format. I have already used it a hundred times before but this time I get this error;

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2020-10-09 15:38:50 [7fb818ed1700] INFO: Opened BCL file '/run/user/1000/gvfs/smb-share:server=192.168.1.129,share=e/1_NextSeq/2020_NextSeq/201007_NB501313_0125_AH5N53BGXF/Data/Intensities/BaseCalls/L001/0318.bcl.bgzf' with 0 clusters
2020-10-09 15:39:01 [7fb80beb7700] ERROR: Thread: 3 caught an exception first: /home/shahlab/miniconda2/conda-bld/bcl2fastq_1497316272077/work/bcl2fastq/src/cxx/lib/io/SyncFile.cpp(166): Throw in function virtual void bcl2fastq::io::UnprocessedFile::logError(std::streamsize, std::streamsize) const
Dynamic exception type: boost::exception_detail::clone_impl **bcl2fastq::common::InputDataError**
std::exception::what: Synchronized file '/run/user/1000/gvfs/smb-share:server=192.168.1.129,share=e/1_NextSeq/2020_NextSeq/201007_NB501313_0125_AH5N53BGXF/Data/Intensities/BaseCalls/L001/0317.bcl.bgzf' truncated: bytes_read=183934 bytes_expected=228035
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError>'
  what():  Synchronized file '/run/user/1000/gvfs/smb-share:server=192.168.1.129,share=e/1_NextSeq/2020_NextSeq/201007_NB501313_0125_AH5N53BGXF/Data/Intensities/BaseCalls/L001/0317.bcl.bgzf' **truncated: bytes_read=183934 bytes_expected=228035**
**Aborted (core dumped)**

So how can I solve this?

Thanks in advance

Answer 1

[GenoMax]

If nothing has changed in your setup then this is really odd. I think you have a corrupt BCL file that is causing this. Try a previous run to make sure your install of bcl2fastq works ok. If it does then I would try deleting 201007_NB501313_0125_AH5N53BGXF/Data/Intensities/BaseCalls/L001/0318.bcl.bgzf file and use --ignore-missing-bcls to see if the processing completes.