bcl2fastq error

Question

[17318598206]

Hello,

I had install bcl2fastq in my Ubuntu 20.04.5 LTS by

$conda install -c bih-cubi bcl2fastq2

and my code is

$bcl2fastq --runfolder /home/data/vip55/1work/guide-seq/220919_E00560_0331_AHJ5W3CCX2 --barcode-mismatches 1 --input-dir /home/data/vip55/1work/guide-seq/220919_E00560_0331_AHJ5W3CCX2/Data/Intensities/BaseCalls -o /home/data/vip55/1work/guide-seq --tiles s_8

but it has a error:

ERROR: bcl2fastq::common::Exception: 2022-Oct-14 09:22:04: No such file or directory (2): /opt/conda/conda-bld/bcl2fastq2_1548424849859/work/src/cxx/lib/layout/FileExistenceVerifier.cpp(212): Throw in function static void bcl2fastq::layout::FileExistenceVerifier::throwException(const string&, bcl2fastq::common::TileAggregationMode, bcl2fastq::common::LaneNumber, bcl2fastq::common::TileNumber)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::IoError>
std::exception::what: Unable to find positions file for lane: 8 and tile: 1101

How to fix it

Thanks in advance for any suggestions!

Best,

Anna

[GenoMax]

As colindaven suggests you should obtain a fresh copy of the data to see if you had a bad copy. If the fresh copy also shows the same error then you can add the option for bcl2fastq

--ignore-missing-positions                      assume [0,i] for missing positions, where i is incremented starting from 0

to get around this error. Some data may become not usable.

[colindaven]

You're missing data from your sequencing run.

Check the data transfer was completed before starting the tool (I've been impatient several times before).

Check the data is consistent. Re-copy the data. Check with the lab there weren't any run failures during the run.

Where did the data come from (sequencer, internet ....) ?