I have a small RNA sequencing run (QIAseq miRNA low input) in
NextSeq 2000 sequencing machine. I have all the related files but when I ran
bcl2fastq --barcode-mismatches 0 in the directory where all the files are, I do get the following error:
ERROR: bcl2fastq::common::Exception: 2022-Mar-07 22:18:49: No such file or directory (2): /sw/apps/bioinfo/bcl2fastq/2.17.1/src/bcl2fastq/src/cxx/lib/data/BclFile.cpp(103): Throw in function static void bcl2fastq::data::BclFile::getAndVerifyFileName(const boost::filesystem::path&, bcl2fastq::common::LaneNumber, bcl2fastq::common::TileNumber, bcl2fastq::common::CycleNumber, bool, boost::filesystem::path&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::IoError> std::exception::what: Unable to find BCL file for 's_1_1101' in: /crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/220202_VH00203_129_AAANKJFM5/Data/Intensities/BaseCalls/L001/C1.1
Based on the post here it seems that
NextSeq 2000 uses
CBCL instead of
BCL. Is there any specific option for
bcl2fastq to specify the method or similar thing to circumvent the error?
Thank you for you comment - could you also please share a quick command of the
Not off hand, a colleague used it once for a similar task when he failed to convert Nextseq 2000 bcls. I recall, the usage is very close to bcl2fastq
Carambakaracho is correct. NS 2K requires
bcl-convertfor data processing. Syntax is very similar to
Be careful with number of threads. Since you have NS 2K data your
bclfiles should be compressed so last two options can be used.
You can run
bcl-convert -hto access in-line help.