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  • bcl2fastq error "No tiles were found to process"

    Hi,

    I am quite a newbie for bcl2fastq software. I obtained my data from NextSeq500 system and trying to run bcl2fastq 2.0 for fastq conversion. But I am always getting error saying that "No tiles were found to process".

    I have 6 same samples in all 4 lanes. I've checked all necessary files and were placed on right directories. I created my sample sheet by using IEM. I try to use different --tiles opt. parameters. Also --no-lane-splitting option with different configurations but nothing works. I read a lot however I haven't seen anyone had this error. So I am kind of afraid that this a basic problem. Could anyone help me to solve this?

    Note: IEM doesn't create a "Lane" column that's why I write that one down. However I also tried with "Lane" as first column addition to samplsesheet below.

    My SampleSheet:

    [Header],,,,,,,,,

    IEMFileVersion,4,,,,,,,,

    Investigator Name,SK,,,,,,,,

    Experiment Name,01.08.17-EXOME-RUN-1,,,,,,,,

    Date,05.10.2017,,,,,,,,

    Workflow,GenerateFASTQ,,,,,,,,

    Application,NextSeq FASTQ Only,,,,,,,,

    Assay,TruSight Enrichment,,,,,,,,

    Description,,,,,,,,,

    Chemistry,Amplicon,,,,,,,,

    ,,,,,,,,,

    [Reads],,,,,,,,,

    76,,,,,,,,,

    76,,,,,,,,,

    ,,,,,,,,,

    [Settings],,,,,,,,,

    Adapter,CTGTCTCTTATACACATCT,,,,,,,,

    ,,,,,,,,,

    [Data],,,,,,,,,

    Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description

    EXOM1,BARAN-CENGIZ,01.08.17-EXOME-RUN-1,A01,N701,TAAGGCGA,E502,ATAGAGAG,Deneme,Deneme

    EXOM2,FERHAT-CEKMEZ,01.08.17-EXOME-RUN-1,A02,N702,CGTACTAG,E502,ATAGAGAG,Deneme,Deneme

    EXOM3,MEHMET-AKIF,01.08.17-EXOME-RUN-1,A03,N703,AGGCAGAA,E502,ATAGAGAG,Deneme,Deneme

    EXOM4,AYSE-ALINA,01.08.17-EXOME-RUN-1,A04,N704,TCCTGAGC,E502,ATAGAGAG,Deneme,Deneme

    EXOM5,CEYHUN-YILMAZ-KAN,01.08.17-EXOME-RUN-1,A05,N705,GGACTCCT,E502,ATAGAGAG,Deneme,Deneme

    EXOM6,CEYHUN-YILMAZ-DOKU,01.08.17-EXOME-RUN-1,A06,N707,CTCTCTAC,E502,ATAGAGAG,Deneme,Deneme

    And error goes like this:

    genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3$ /usr/local/bin/bcl2fastq --runfolder-dir /media/demo/170815_NB501568_0002_AH257CBGX3 --output-dir /media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls

    BCL to FASTQ file converter

    bcl2fastq v2.20.0.422

    Copyright (c) 2007-2017 Illumina, Inc.

    2017-10-14 07:38:54 [1816880] Command-line invocation: /usr/local/bin/bcl2fastq --runfolder-dir /media/demo/170815_NB501568_0002_AH257CBGX3 --output-dir /media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls

    2017-10-14 07:38:54 [1816880] INFO: Minimum log level: INFO

    2017-10-14 07:38:54 [1816880] INFO: Sample sheet: '/media/demo/170815_NB501568_0002_AH257CBGX3/SampleSheet.csv'

    2017-10-14 07:38:54 [1816880] INFO: Runfolder path: '/media/demo/170815_NB501568_0002_AH257CBGX3'

    2017-10-14 07:38:54 [1816880] INFO: Input path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/'

    2017-10-14 07:38:54 [1816880] INFO: Intensities path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/'

    2017-10-14 07:38:54 [1816880] INFO: Output path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls'

    2017-10-14 07:38:54 [1816880] INFO: InterOp path: '/media/demo/170815_NB501568_0002_AH257CBGX3/InterOp/'

    2017-10-14 07:38:54 [1816880] INFO: Stats path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/Stats/'

    2017-10-14 07:38:54 [1816880] INFO: Reports path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/Reports/'

    2017-10-14 07:38:54 [1816880] INFO: Detected CPUs: 16

    2017-10-14 07:38:54 [1816880] INFO: Loading threads: 4

    2017-10-14 07:38:54 [1816880] INFO: Processing threads: 16

    2017-10-14 07:38:54 [1816880] INFO: Writing threads: 4

    2017-10-14 07:38:54 [1816880] INFO: Allowed barcode mismatches: 1

    2017-10-14 07:38:54 [1816880] INFO: Tiles: <all>

    2017-10-14 07:38:54 [1816880] INFO: Minimum trimmed read length: 35

    2017-10-14 07:38:54 [1816880] INFO: Use bases masks: <none>

    2017-10-14 07:38:54 [1816880] INFO: Mask short adapter reads: 22

    2017-10-14 07:38:54 [1816880] INFO: Adapter stringency: 0.9

    2017-10-14 07:38:54 [1816880] INFO: Adapter trimming method: Allow matches with indels

    2017-10-14 07:38:54 [1816880] INFO: Ignore missing BCLs: NO

    2017-10-14 07:38:54 [1816880] INFO: Ignore missing filters: NO

    2017-10-14 07:38:54 [1816880] INFO: Ignore missing positions: NO

    2017-10-14 07:38:54 [1816880] INFO: Ignore missing controls: NO

    2017-10-14 07:38:54 [1816880] INFO: Include non-PF clusters: NO

    2017-10-14 07:38:54 [1816880] INFO: Create FASTQs for index reads: NO

    2017-10-14 07:38:54 [1816880] INFO: Use bgzf compression for FASTQ files: YES

    2017-10-14 07:38:54 [1816880] INFO: FASTQ compression level: 4

    2017-10-14 07:38:54 [1816880] INFO: RunInfo.xml: '"/media/demo/170815_NB501568_0002_AH257CBGX3/RunInfo.xml"'

    2017-10-14 07:38:54 [1816880] INFO: Lane: 1

    2017-10-14 07:38:54 [1816880] INFO: Mask:

    2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

    2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167, 168

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Lane: 2

    2017-10-14 07:38:54 [1816880] INFO: Mask:

    2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

    2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Lane: 3

    2017-10-14 07:38:54 [1816880] INFO: Mask:

    2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

    2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles:

    93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Lane: 4

    2017-10-14 07:38:54 [1816880] INFO: Mask:

    2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

    2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

    2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

    2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

    2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

    2017-10-14 07:38:54 [1816880] INFO: Cycles:

    93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

    2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

    2017-10-14 07:38:54 [1816880] ERROR: bcl2fastq::common::Exception: 2017-Oct-14 07:38:54: Success (0): /TeamCityBuildAgent/work/556afd631a5b66d8/src/cxx/lib/layout/Layout.cpp(1194): Throw in function static void bcl2fastq::layout::TileLayoutDetector::detectTileLayout(const std::vector<std::basic_string<char> >&, const bcl2fastq::layout::RunInfoXml&, const bcl2fastq::config::SampleSheetCsv&, const boost::filesystem:ath&, std::vector<bcl2fastq::layout::laneinfo>&, bcl2fastq::common::TileFileMap&, bcl2fastq::common::NumBasesPerByte&, bcl2fastq::common::TileAggregationMode, bool, bcl2fastq::common::CycleNumber, bcl2fastq::common::CycleNumber, bool) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::inputdataerror> std::exception::what: No tiles were found to process.

  • #2
    I've had pretty good luck getting support directly from Illumina for issues like this, you might contact them and send the logs.

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