Dear all,
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.
Thank you for you comment - could you also please share a quick command of the
bclconvert
?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-convert
for data processing. Syntax is very similar tobcl2fastq
.Be careful with number of threads. Since you have NS 2K data your
bcl
files should be compressed so last two options can be used.You can run
bcl-convert -h
to access in-line help.