bcl2fastq error with RunInfo.xml

Question

[Apex92]

Dear all,

I am running to an error with bcl2fastq. I have slightly different setup - I have received ONLY two files from the sequencing company in order to run conversion.

One of the files is in tar.gz.dm5 which contains a single line:

daac12b61f03f01d303f7b47f9118994  220202_VH00203_129_AAANKJFM5.tar.gz

and the other file is the main file with 24G size named 220202_VH00203_129_AAANKJFM5.tar.gz and the head is:

220202_VH00203_129_AAANKJFM5/0002770000375500021710000000000014207667464015153 5ustar  hiseq.bioinfohiseq220202_VH00203_129_AAANKJFM5/Config/0002770000375500021710000000000014176461545016355 5ustar  hiseq.bioinfohiseq220202_VH00203_129_AAANKJFM5/Config/nextseq1k2k-calibration.cfg0000660000375500021710000001777314176461544023520 0ustar  hiseq.bioinfohiseq[AlignmentConfig]
CalibratedSurfaceFindingCenterZMicrometers = 755                                                    ; Calibration; Surface Finding Center Z in um.
SampleTiltBottomThetaX = 0                                                                          ; Calibration; This is the calculated (X) sample tilt angle in mrad as part of camera tilt test routine for Bottom Surface
SampleTiltBottomThetaY = 0                                                                          ; Calibration; This is the calculated (Y) sample tilt angle in mrad as part of camera tilt test routine for Bottom Surface
SampleTiltTopThetaX = 0                                                                             ; Calibration; This is the calculated (X) sample tilt angle in mrad as part of camera tilt test routine for Top Surface
SampleTiltTopThetaY = 0                                                                             ; Calibration; This is the calculated (Y) sample tilt angle in mrad as part of camera tilt test routine for Top Surface
TestStationTiltThetaX = 0                                                                           ; Calibration; This is the calculated (X) test station tilt angle in mrad as part of test station tilt calibration routine
TestStationTiltThetaY = 0                                                                           ; Calibration; This is the calculated (Y) test station tilt angle in mrad as part of test station tilt calibration routine
ThetaX = -0.116812703440842                                                                         ; Calibration; This is the average (X) camera tilt in mrad to be corrected for in autotilt
ThetaY = 0.0794609426404551                                                                         ; Calibration; This is the average (Y) camera tilt in mrad to be corrected for in autotilt

I created a SampleSheet.csv file for the conversion and when I run the bcl2fastq --barcode-mismatches 0 at the same directory I do get an error related to RunInfo.xml.

BCL to FASTQ file converter
bcl2fastq v2.17.1.14
Copyright (c) 2007-2015 Illumina, Inc.

2022-03-07 19:42:22 [2b5ea55e2d00] Command-line invocation: bcl2fastq --barcode-mismatches 0 
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Minimum log level: INFO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Sample sheet: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/SampleSheet.csv'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Runfolder path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Input path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/Data/Intensities/BaseCalls/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Intensities path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/Data/Intensities/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Output path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/Data/Intensities/BaseCalls/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: InterOp path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/InterOp/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Stats path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/Data/Intensities/BaseCalls/Stats/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Reports path: '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/Data/Intensities/BaseCalls/Reports/'
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Detected CPUs: 40
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Loading threads: 4
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Processing threads: 40
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Demultiplexing threads: 8
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Writing threads: 4
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Aggregated tiles: AUTO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Allowed barcode mismatches: 0 
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Tiles: <ALL>
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Minimum trimmed read length: 35
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Use bases masks: <NONE>
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Mask short adapter reads: 22
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Adapter stringency: 0.9
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Ignore missing BCLs: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Ignore missing filters: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Ignore missing positions: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Ignore missing controls: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Include non-PF clusters: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: Create FASTQs for index reads: NO
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: FASTQ compression level: 4
2022-03-07 19:42:22 [2b5ea55e2d00] INFO: RunInfo.xml: '"/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/RunInfo.xml"'
2022-03-07 19:42:22 [2b5ea55e2d00] ERROR: bcl2fastq::common::Exception: 2022-Mar-07 19:42:22: No such file or directory (2): /sw/apps/bioinfo/bcl2fastq/2.17.1/src/bcl2fastq/src/cxx/lib/io/Xml.cpp(193): 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 '/crex/proj/snic2020-16-229/Toxoplasma_bcl_delivery05646/INBOX/P23001/RunInfo.xml' file for reading

Has anyone experience with this type of conversion to help me how to solve this? I believe that RunInfo information should also be in the 220202_VH00203_129_AAANKJFM5.tar.gz file but I do not know how to solve this problem.

Thank you in advance.

[swbarnes2]

Wow. How lazy of the sequencing company not to run bcl2fastq for you. Illumina files are their bread and butter, they should be using their expertise to do this instead of passing it off to someone who doesn't really need to know how to do that.

I think you need to google to find a command that will show you what files are in the tar; I suppose it's possible that the RunInfo just isn't there.

[Janki]

How were you able to resolve this? I am running into the same error now..