bcl2fastq error

Question

[Tao]

2022-01-20 18:48:36 [7fc7200de7c0] ERROR: bcl2fastq::common::Exception: 2022-Jan-20 18:48:36: No such file or directory (2): /home/shahlab/miniconda2/conda-bld/bcl2fastq_1497316272077/work/bcl2fastq/src/cxx/lib/io/Xml.cpp(201): Throw in function boost::property_tree::ptree bcl2fastq::io::parseXmlFile(const boost::filesystem::path&)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::IoError>
std::exception::what: Unable to open '/public/home/zhangzhh/01_rawdata/09_normal/80-857152069/N2200458_80-857152069_Lib/220114_A00212_0102_BH3NTMDSX3/Data/Intensities/BaseCalls/RunInfo.xml' file for reading

Does anyone know why this error occurs?

[cpad0112]

Check if this file exists '/public/home/zhangzhh/01_rawdata/09_normal/80-857152069/N2200458_80-857152069_Lib/220114_A00212_0102_BH3NTMDSX3/Data/Intensities/BaseCalls/RunInfo.xml' and user has permissions to read this file.

Answer 1

[GenoMax]

Error message is pretty clear. bcl2fastq is not able to open the file mentioned in the error message. Does the account you are running this from have read read privileges there?

Problem may actually be in the bcl2fastq command you are using which you are not showing us. So you will want to do that.