Hi everyone,

We have NextSeq 550 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. This is my code:

bcl2fastq \
-R /proj/naiss2023-6-366/seq_04052024 \
--input-dir /proj/naiss2023-6-366/seq_04052024/Intensities/BaseCalls \
--output-dir /proj/naiss2023-6-366/seq_04052024/output \
--interop-dir /proj/naiss2023-6-366/seq_04052024/interop \
--stats-dir /proj/naiss2023-6-366/seq_04052024/stats \
--reports-dir /proj/naiss2023-6-366/seq_04052024/reports \
--sample-sheet 'SampleSheet.csv' \
-r 4 -p 40 -w 4 \
--minimum-trimmed-read-length 35 \
--mask-short-adapter-reads 22 \
--adapter-stringency 0.9 \
--ignore-missing-bcls \
--ignore-missing-filter \
--ignore-missing-positions \
--no-lane-splitting
--ignore-missing-bcl 
—ignore-missing-control
 --ignore-missing-stats"

I got this error:

CycleBCIFile::openFile(const boost::filesystem::path&, bcl2fastq::common::LaneNumber, bcl2fastq::common::CycleNumber)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError>
std::exception::what: Unable to read header of cycle BCI file '/proj/naiss2023-6-366/seq_04052024/Intensities/BaseCalls/L001/0001.bcl.bgzf.bci': bytes_read=0 bytes_expected=8

terminate called after throwing an instance of 'boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError>'
  what():  Unable to read header of cycle BCI file '/proj/naiss2023-6-366/seq_04052024/Intensities/BaseCalls/L001/0001.bcl.bgzf.bci': bytes_read=0 bytes_expected=8
Aborted (core dumped)

In the output folder the fastq file generate but contain nothing and just the name of file. it would be appritiated if you could help me.